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BIOL 2604 > Microbial Genetics > Flashcards

Microbial Genetics Flashcards

(80 cards)

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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
Replication Fork
-where the two strands of DNA are separated and the new strands of DNA are synthesized.
26
Process of Replication
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!
27
What does the DNA gyrase do?
-uncoil DNA
28
Why does replication go in different directions?
-because it is faster and takes half the amount of time to make a chromosome.
29
What happens to Okazaki fragments?
-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
30
What does DNA ligase do?
-seals the nick!
31
How are Okazaki Fragments fussed together?
-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
32
What happens during transcription?
-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
33
What are operons?
-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
What are operons used for?
-efficient way to expression multiple genes at once
35
What do operons transcript to?
-operons transcript to polycistronic mRNA -ORF = open reading frame
36
What does 1 gene equal?
-mono-cistronic
37
What type of operon does E. Coli have?
-histidine biosynthesis operon
38
RNA Polymerase (RNAP)
-Bacterial RNAP -Eukaryotic RNAP -promoters contain sequences that are recognized by sigma factors -have bases from -10 to -35 sequences
39
Bacterial RNAP
-one core enzyme (4 essential subunits) -PLUS a SIGMA subunit -Fast
40
Eukaryotic RNAP
-many subunits plus other required transcription factors proteins -Slow
41
Sigma Factors
-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
Sigma 70
-For most genes, major sigma factor for normal growth. -TTGACA
43
Translation - Eukaryotes and Archaea
-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
What two do transcription the same and who does it differently?
-Eukaryotes and Archaea do it the same -Bacteria do it differently
45
Gene Structure of Bacterial
-Operons -y promoter - (-10) and (-35) sequence bases
46
Gene Structure of Archaeal
-operons -promoters
47
Gene Structure of Eukaryotic
-No operons -promoters = TATA
48
What does an Operon in the DNA produce and what two do this?
-produces a polycistronic mRNA -bacteria and archaea -look at notes
49
What do single genes transcribed alone produce and who does this?
-produces monocistronic mRNAs -Eukaryotes -look at notes
50
Polycistronic
-produces multiple protein products
51
Monocistronic
-contain the coding sequence for only one protein
52
Transcription: Prokaryotes
-very little non-coding DNA -virtually no mRNA processing -Transcription and translation are coupled -look at notes
53
Transcription: Eukaryotes
-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
Between introns and exons which ones are coding and which ones are not coding?
-introns are non-coding -Extron's are coding
55
Transcription of Eukaryotic
-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
Translation of Eukaryotes
-Mature mRNA transported to cytoplasm -has a poly A tail -translated to form a protein
57
Translation (mRNA -> protein)
-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
Ribosomes
-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
rNA
-binds to mRNA and -creates peptide bonds
60
tRNA
-serves as "decoder" between mRNA and amino acid -codons in mRNA are decoded by anticodons in tRNA
61
What do antibiotics target?
-The ribosomes
62
Why does a tRNA exists?
-to read each codon and -each tRNA is "charged" (covalently linked) to the proper amino acid encoded by that codon. -look at notes
63
What is a polysome?
-a complex of multiple ribosomes bound to a single mRNA molecule during translation. -look at notes
64
In Bacteria and Archaea, ribosomes bind to...
-sequences in mRNA called... -"Shine-Dalgarno sequences" or "Ribosome-Binding Sites" (RBS) -these sequences resemble AGGAGG (core) -variation can determine strength of translation
65
Where does translation start?
-at start codon (AUG or GUG) just downstream of RBS in mRNA
66
What are the first amino acids in bacteria, archaea, and eukaryotes
-N-formyl methionine in Bacteria -methionine in Archaea and Eukaryotes
67
What does translation continue through?
-hundreds of codons, adding one amino acid to the new protein at each codon.
68
Whan is translation terminated?
-at the stop codon sequences -UAA, UAG, UGA in mRNA -no tRNA
69
Translation: Bacterial and Archaea
-start at RBS on mRNA and stop at UAA -make protein product
70
Can ribosome binding sites be strong or weak?
-They can be both. -it effects the strength of translation
71
Translation: Eukaryotic
-starts at cap on mRNA and ends at UAA -cap tells where to start and is a modification -makes a protein product
72
Translation things for Bacterial
-RBS -No mRNA processing -N-formyl methionine
73
Translation things for Archaeal
-RBS -methionine -No mRNA processing
74
Translation things for Eukaryotic
-Cap AUG -methionine -mRNA processing
75
Which do coupled transcription and translation and who do not and why?
-Bacterial and archaea do coupled transcription and translation. -Eukaryotic does not because it is more complex -prokaryotes do because of growth rates
76
Protein Folding
-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
Can proteins fold a lone and can properly folded proteins unfold?
-most proteins can fold a lone, but some cannot -properly folded proteins become unfolded either spontaneously or due to heat/chemicals.
78
What happens to misfolded proteins?
-can be aided in proper folding by "Chaperons" such as Dna K/J and GroEL/ES (this requires atp) -look at notes
79
Protein Export
-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
What system can export a certain fully-folded proteins?
-The Twin-Arginine System (TAT system) -look at notes

BIOL 2604 (17 decks)

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