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BIOL 2604 > Microbial Genetics > Flashcards

Microbial Genetics Flashcards

1
Q

The Central Dogma

A

-The process in which DNA is replicated, then transcript to mRNA, and then translated to a protein.

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2
Q

Synthesis of the three types of informational molecules

A

-Replication
-Transcription
-Translation

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3
Q

Replication

A

-both strands are templates for new DNA synthesis
-DNA strands split and make new one

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4
Q

Translation

A

-messenger RNA is template for protein synthesis (happens in ribosome)
-look in notebook

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5
Q

Transcription

A

-one strand is a template for RNA synthesis
-Look in notebook

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6
Q

DNA Structure Bacterial

A

-circular
-prokaryote
-supercoiled
-plasmids

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7
Q

DNA Structure Archaeal

A

-circular
-prokaryote
-supercoiled
-plasmids

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8
Q

DNA Structure Eukaryotic

A

-Linear
-eukaryote
-supercoiled
-plasmids (very rare)

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9
Q

Bacterial Chromosome Supercoiling

A

-relaxed circular DNA (double strand) then breaks one strand
-Now there is a relaxed nick circular DNA that then rotates one end of the broken strand around helix and seal.
-It is now supercoiled circular DNA
-chromosomal DNA with supercoiled domains
-Look at notes!

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10
Q

What is supercoiling use for?

A

-to store a large amount of DNA in a tiny space
-When DNA is supercoiled translations and transcription cannot occur.

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11
Q

What is DNA replicarion?

A

-Semiconservative
-Look at notes

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12
Q

DNA Polymerases

A

-Pol III
-DNA Replication is carried out by polymerases
-ALL DNA polymerases require an RNA primer to initiate synthesis
-DNA polymerases are involved in a variety of mechanisms used to repair damaged DNA.
-Make copies of chromosomes
-Look at notes

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13
Q

Why do DNA polymerases have proofreading ability?

A

-to insure fidelity of DNA replication

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14
Q

What things are involved in DNA replication?

A

-Helicase (enzyme)
-Primase
-Single-strand binding protein
-DNA poly III
-Okazaki fragments
-Look at notes

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15
Q

What does a helicase do?

A

-splits DNA in half
-unbinding it

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16
Q

What are the two strands that come after the helicase splits the DNA?

A

-Leading strand
-Lagging strand

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17
Q

What way does poly I work?

A

-only works from 5’ to 3’

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18
Q

What is the lagging strand?

A

-this strand is synthesized occurs is a discontinuous manner creating Okazaki fragments
-It does this because pol I can only work a certain way and because of the replication fork
-look at notes

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19
Q

What happens during DNA Replication?

A
  • Dna A protein recognizes the origin and recruits other proteins
    -DNA synthesis is ALWAYS 5’ to 3’
    -creating lagging and leading strands
    -look at notes
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20
Q

What fuses Okazaki Fragments together?

A

-ligase

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21
Q

Where does DNA synthesis start at?

A

-origin of replication

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22
Q

what type of origin do prokaryotes have?

A

-single origin on the single circular chromosome

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23
Q

what type of origin do eukaryotes have?

A

-many origins on each linear chromosome

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24
Q

What form is replication in?

A

-“theta-form”
-usually bidirectional

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25
Q

Replication Fork

A

-where the two strands of DNA are separated and the new strands of DNA are synthesized.

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26
Q

Process of Replication

A
  1. replisome binds and initiates synthesis
  2. replication fork continuous synthesis in opposite direction
  3. replication forks hit terminus of replication and collide, releasing two chromosome copies
    -Look at notes!
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27
Q

What does the DNA gyrase do?

A

-uncoil DNA

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28
Q

Why does replication go in different directions?

A

-because it is faster and takes half the amount of time to make a chromosome.

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29
Q

What happens to Okazaki fragments?

A

-RNA primers start to fill in the gaps between Okazaki Fragments.
-Exonuclease to remove RNA
-DNA polymerase to fill in behind
-DNA ligase
-look at notes

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30
Q

What does DNA ligase do?

A

-seals the nick!

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31
Q

How are Okazaki Fragments fussed together?

A

-RNA primer on one end of DNA and DNA poly III on the other
-poly III makes DNA and then poly I replaces it and primer goes away
-poly I is then replaced by DNA ligase and fusses fragments together
-look at notes

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32
Q

What happens during transcription?

A

-RNA polymerase and sigma recognizes promoter and initiation site.
-Transcription begins, sigma is released and RNA chain grows
-the RNA polymerase separates the DNA strands
-termination site reached, chain growth stops
-polymerase and RNA released
-look at notes

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33
Q

What are operons?

A

-transcription units
-group of genes located next to each other on DNA
-three main parts: structural genes, operator region, and the promoter
-look at notes

34
Q

What are operons used for?

A

-efficient way to expression multiple genes at once

35
Q

What do operons transcript to?

A

-operons transcript to polycistronic mRNA
-ORF = open reading frame

36
Q

What does 1 gene equal?

A

-mono-cistronic

37
Q

What type of operon does E. Coli have?

A

-histidine biosynthesis operon

38
Q

RNA Polymerase (RNAP)

A

-Bacterial RNAP
-Eukaryotic RNAP
-promoters contain sequences that are recognized by sigma factors
-have bases from -10 to -35 sequences

39
Q

Bacterial RNAP

A

-one core enzyme (4 essential subunits)
-PLUS a SIGMA subunit
-Fast

40
Q

Eukaryotic RNAP

A

-many subunits plus other required transcription factors proteins
-Slow

41
Q

Sigma Factors

A

-different sigma factors recognize different promoters
-Ex. low nitrogen, so need 30 genes to turn on, call on sigma factors to activate all the genes, sigma 54

42
Q

Sigma 70

A

-For most genes, major sigma factor for normal growth.
-TTGACA

43
Q

Translation - Eukaryotes and Archaea

A

-have DNA with B recognition (BRE), TATA, and transcription initiation site (Init) that make up the promoter
-it then binds to TATA binding protein (TBP) and Transcription factor B (TFB), start of transcription
-then binding of RNA polymerase
-transcription, look at notes

44
Q

What two do transcription the same and who does it differently?

A

-Eukaryotes and Archaea do it the same
-Bacteria do it differently

45
Q

Gene Structure of Bacterial

A

-Operons
-y promoter
- (-10) and (-35) sequence bases

46
Q

Gene Structure of Archaeal

A

-operons
-promoters

47
Q

Gene Structure of Eukaryotic

A

-No operons
-promoters = TATA

48
Q

What does an Operon in the DNA produce and what two do this?

A

-produces a polycistronic mRNA
-bacteria and archaea
-look at notes

49
Q

What do single genes transcribed alone produce and who does this?

A

-produces monocistronic mRNAs
-Eukaryotes
-look at notes

50
Q

Polycistronic

A

-produces multiple protein products

51
Q

Monocistronic

A

-contain the coding sequence for only one protein

52
Q

Transcription: Prokaryotes

A

-very little non-coding DNA
-virtually no mRNA processing
-Transcription and translation are coupled
-look at notes

53
Q

Transcription: Eukaryotes

A

-Have lots of noncoding DNA
-Produce only monocistronic mRNA
-Extensively process mRNA (5’ Cap, introns removed, exons spliced together, 3’ poly A tail)
-Transcription is in the nucleus and translation is in the cytoplasm
-Not coupled
-look at notes

54
Q

Between introns and exons which ones are coding and which ones are not coding?

A

-introns are non-coding
-Extron’s are coding

55
Q

Transcription of Eukaryotic

A

-DNA with exon and introns transcript
-then primary RNA transcript, RNA processing, cap and tail added and introns excised
-mature mRNA with cap and tail formed
-move to cytoplasm

56
Q

Translation of Eukaryotes

A

-Mature mRNA transported to cytoplasm
-has a poly A tail
-translated to form a protein

57
Q

Translation (mRNA -> protein)

A

-highly conserved across prokaryotes and eukaryotes
-utilizes an (almost) Universal, triplet, genetic code (three units TTA)
-takes place within ribosomes (three rRNA molecules plus >40 protein)

58
Q

Ribosomes

A

-30S + 50S subunits = 70S in prokaryotes
-40S + 60S subunits = 80S in eukaryotes
-small and large subunits of ribosomes (look at notes)
-S = Svedberg Unit

59
Q

rNA

A

-binds to mRNA and
-creates peptide bonds

60
Q

tRNA

A

-serves as “decoder” between mRNA and amino acid
-codons in mRNA are decoded by anticodons in tRNA

61
Q

What do antibiotics target?

A

-The ribosomes

62
Q

Why does a tRNA exists?

A

-to read each codon and
-each tRNA is “charged” (covalently linked) to the proper amino acid encoded by that codon.
-look at notes

63
Q

What is a polysome?

A

-a complex of multiple ribosomes bound to a single mRNA molecule during translation.
-look at notes

64
Q

In Bacteria and Archaea, ribosomes bind to…

A

-sequences in mRNA called…
-“Shine-Dalgarno sequences” or “Ribosome-Binding Sites” (RBS)
-these sequences resemble AGGAGG (core)
-variation can determine strength of translation

65
Q

Where does translation start?

A

-at start codon (AUG or GUG) just downstream of RBS in mRNA

66
Q

What are the first amino acids in bacteria, archaea, and eukaryotes

A

-N-formyl methionine in Bacteria
-methionine in Archaea and Eukaryotes

67
Q

What does translation continue through?

A

-hundreds of codons, adding one amino acid to the new protein at each codon.

68
Q

Whan is translation terminated?

A

-at the stop codon sequences
-UAA, UAG, UGA in mRNA
-no tRNA

69
Q

Translation: Bacterial and Archaea

A

-start at RBS on mRNA and stop at UAA
-make protein product

70
Q

Can ribosome binding sites be strong or weak?

A

-They can be both.
-it effects the strength of translation

71
Q

Translation: Eukaryotic

A

-starts at cap on mRNA and ends at UAA
-cap tells where to start and is a modification
-makes a protein product

72
Q

Translation things for Bacterial

A

-RBS
-No mRNA processing
-N-formyl methionine

73
Q

Translation things for Archaeal

A

-RBS
-methionine
-No mRNA processing

74
Q

Translation things for Eukaryotic

A

-Cap AUG
-methionine
-mRNA processing

75
Q

Which do coupled transcription and translation and who do not and why?

A

-Bacterial and archaea do coupled transcription and translation.
-Eukaryotic does not because it is more complex
-prokaryotes do because of growth rates

76
Q

Protein Folding

A

-the newly translated protein must fold into the proper secondary and tertiary structure in order to be functional.
-The information required for proper folding is built into the primary amino acid sequence for most proteins.

77
Q

Can proteins fold a lone and can properly folded proteins unfold?

A

-most proteins can fold a lone, but some cannot
-properly folded proteins become unfolded either spontaneously or due to heat/chemicals.

78
Q

What happens to misfolded proteins?

A

-can be aided in proper folding by “Chaperons” such as Dna K/J and GroEL/ES (this requires atp)
-look at notes

79
Q

Protein Export

A

-some proteins must exit the cell into the medium or periplasm
-These proteins have a hydrophobic “signal sequence” that inserts in the membrane.
-They are exported in unfolded form via the “Sec system” and fold on the outside.
-look at notes

80
Q

What system can export a certain fully-folded proteins?

A

-The Twin-Arginine System (TAT system)
-look at notes

BIOL 2604 (17 decks)

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