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BIOL > Molecular Microbiology 8-11 > Flashcards

Molecular Microbiology 8-11 Flashcards

1
Q

What is tRNA?

A
  • tRNA is specific to recognizing each amino acid
  • Binds with ATP to an amino acid-producing AMP
  • its anticodon loop binds to the complementary codon on mRNA
  • the 3’ acceptor arm ester bonds with the carboxylic acid of an amino acid and carries it to the ribosome site
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2
Q

What is mRNA?

A

-During transcription an RNA Polymerase reads DNA and creates a complementary single RNA strand called mRNA.
-mature mRNA after splicing of exons determines the sequence of amino acids to be formed as a protein

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3
Q

What is rRNA?

A

-non-coding RNA that forms the large and small subunits of the Ribosome
-In the larger subunit, it forms the peptidyl transferase, an ENZYME, that catalyzes the peptide bond formation between amino acids in protein biosynthesis (23S rNA). It also allows tRNA hydrolysis to release the protein from the tRNA and Ribosome. (can be targeted by antibiotics so bonds can’t form)

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4
Q

23 sRNA

A

RNA that acts as an ENZYME, not a protein, to catalyze peptide bond formation

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5
Q

Initiation

A

-at AUG start codon major and minor rRNA subunits combine into a ribosome
-Binding site upstream from start codon at GTP cap
-The initiator tRNA, carrying the first amino acid (METhionine), binds to the P-site (peptidyl site) on the Ribosome forming Initiation Complex

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6
Q

Anticodon

A

-Arm of tRNA clover structure that binds to 3 complementary bases of mRNA
-Wobble Hypothesis: binds more loosely to 3rd codon allowing one tRNA to bind to more than one codon and code for the same amino acid

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7
Q

Anticodon

A

-Arm of tRNA clover structure that binds to 3 complementary bases of mRNA
-Wobble Hypothesis: binds more loosely to 3rd codon allowing one tRNA to bind to more than one codon and code for the same amino acid

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8
Q

Elongation

A

-the incoming tRNA anticodon binds to the A-site of the codon next to the P-site
-The ribosome moves along the mRNA in the 5’ to 3’ direction allowing the amino acids to be linked by peptide bonds in the proper direction
-mRNA sifts down a codon and the empty tRNA moves out of the P-site to exit via the E-site

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9
Q

Termination

A

-Once the stop codon reaches the ribosome A-site, Release Factors (RF) cleave polypeptide from tRNA by adding a water
-Ribosome dissociates

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10
Q

GTP

A

Used in translation to form peptide amino acid chains in elongation and other steps

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11
Q

What is a Suppressor?

A

-A mutant tRNA that recognizes when a mRNA is wrong and if there is a stop codon brings an amino acid anyway.
-Compensates for original mutation

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12
Q

What are the Parts of the Amino Acid and what give it it’s properties?

A

(Amino Group, Carboxylic Acid = all have it) and R-Group (changes based on amino acid and can be polar, np ect.)

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13
Q

Gram Positive

A

Stain Purple, 1 membrane with thick membrane
Stain gets stuck in the thick cross-linked peptidoglycan cell wall

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14
Q

Gram Negative

A

Stain Pink, 2 membranes with thin peptidoglycan. Ethanol decolorizer breaks down thin membrane so violet-iodine crystal can escape

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15
Q

Reversion

A

A mutation in the DNA portion that corrects for a mutation
-DNA changing (phenotype might not change back bc epigenetics)

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16
Q

Revertant

A

strain for mutation that restores original phenotype
Same-site: mutation at same site as original
Second-site: mutation at different site

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17
Q

Truncated Protein

A

An amino acid chain that has been shortened because of a mutation - usually nonsense

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18
Q

Silence Mutation

A

A point mutation in the DNA that doesn’t change the amino acid chain produced -nucleotide different, but codon codes for same amino acid

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19
Q

Nonsense Mutation

A

A mutation that changes an amino acid to a stop codon so the protein chain ends early - point

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20
Q

Missense Mutation

A

A mutation that causes one of the amino acids to be changed in a change - point

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21
Q

Frameshift Mutation

A

An insertion or deletion of a nucleotide will shift the entire codon reading down or up and subsequently change the whole protein.
- often results in loss of protein function

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22
Q

Selectable Mutation

A
  • a mutation that has an advantage over a parent
    Something easy to isolate. Phenotypic level- you can see it
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23
Q

Non Selectable Mutation

A
  • mutation that doesn’t have an advantage
  • DNA level- can’t see mutation easily
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24
Q

Ames Test

A

Purpose: test to determine if something is a mutagen and how much it affects

Procedure: Plate strains on different media plates with a little of the nutrients needed to survive. In one plate place chemical being tested. If the plate with the chemical causes more colonies to grow, it is a mutagen bc it caused strain to mutate DNA and grow

-Sometimes mutagen can be created by a chemical modified by another thing. i. e. digestion through liver

25
Q

Mutagenesis

A
26
Q

Mutagens

A

Anything that can cause a mutation,
chemical, physical, biological

27
Q

Nucleotide Base Analog

A

A fake nucleotide base that is similar to the real one and inserts itself into the DNA
-like thymine methyl being replaced by a Bromine

28
Q

Chemical Modification

A

chemical mutagens that cause chemical modifications: Ex Nitrosoguanidine or Oxygen (produce toxic oxygen radicals reacting to DNA)

29
Q

Intercalating Agents

A
  • Something that interrupts the DNA and causes a frameshift mutation
  • like a flat disk that slots itself in between nucleotides
  • ethidium bromide: a type of dye that stains DNA
30
Q

Auxotroph

A

An organism that can’t produce a protein that it needs to survive
- will not grow without it
- notated with a negative sign
- useful in determining mutagens with Ames Test

31
Q

Screening - Negative Selection

A

-Used for non selectable mutations
- replica plating:
-grow colonies on a primary plate
-use a printing block to stamp secondary plates with identical colonies in the same location on plates with different media/nutrients
- Compare plates to find mutant colonies: Find auxotroph and antibacterial resistance mainly

32
Q

Negative Selection

A

Technique used to isolate colonies with specific genetic mutations by eliminating/inhibiting the growth of strains with unwanted characteristics

33
Q

Positive Selection

A

Technique used to select for specific genetic mutations traits by providing a growth advantage/selective pressure for strains with the trait

34
Q

Induced Mutation

A

Mutations made environmentally or purposefully
-Ex: interaction with oxygen radicals or radiation

35
Q

Spontaneous Mutation

A

Those that occur without external cause.

36
Q

F- cell

A

Does not have F plasmid

37
Q

F+ Cell

A

Has the F plasmid and F genome (they are separate)

38
Q

HFr

A

Has the F plasmid and genome combined

39
Q

F- and F+ mating

A

The F plasmid donor cell (F+) gives the whole plasmid to F- and which makes the recipient F+. F- can never be F- again.

40
Q

What types of cells can be donors?

A

Hfr and F+ cells

41
Q

What is conjugation?

A
42
Q

Hfr (Donor) x F- (Recipient) =

A

= F+ and Hfr

43
Q

F+ x F- =

A

= 2 F+

44
Q

Hfr mating with F-

A

Donates part of the F plasmid and all of the genome except for F+ gene.

45
Q

Hfr x F+

A

= Can’t happen (2 donors)

46
Q

What is the order the genes will transfer in?

A

Opposite the arrow direction

47
Q

Function of RecA

A

aka recombinase
-catalyzes recombination of DNA in DNA Repair
-works in SOS System

48
Q

Restriction Enzymes

A

-Usually reads 6 nucleotides (4 is too small of pieces) (8 is too large of pieces)
-Reads genome palindromes = The inverse nucleotide sequence letters GAATTC
-Useful for Cell Defense by recognizing and cleaving foreign DNA

49
Q

EcoRI

A

Palindrome results in single stranded “sticky” ends that DNA ligase repairs into the Double Strand DNA
-Always cuts at G

50
Q

EcoRV

A

Palindrome results in double-stranded “blunt” ends that can be put together with other blunt ends.
-Can insert any DNA in breakage because the breaks act as a template for a fix

51
Q

Polymerase Chain Reaction

A

-individual dna replication technique
- Needs a template strand
-requires a primer (to target a specific gene)
- if double strand, use heat to separate the strands (must be melting temp) (annealing temp)
-taq polymerase is a dna polymerase (it is used because it resists heat)
-Dntp is added (base pairs; material used)
-Taq enzyme now elongates primer and synthesizes complementary strand
-After one cycle you get 2 pieces of dna
-Taq polymerase can be reused and do another round (in the same tube)
-Used to exponentially increase the number of DNA purely to see if it is present (qualitative)
-Ran before Gel electrophoresis

52
Q

Dntp

A

The artificial base pairs A, T, C, G taken by taq polymerase to allow replication

53
Q

Gel Electrophoresis

A

-Separates DNA based on size
-DNA is negatively charged so when an electric current is passed through gel with DNA, it is attracted to the positive side
-Large pieces of DNA move slowly
-Small pieces of DNA move faster and will make it to the end of the gel quicker.
-Use a DNA ladder as a reference for DNA piece movement

54
Q

F Plasmid

A

Has all genes required for self-replication

55
Q

Specialized v Generalized Transduction

A

Specialized, at specific spots and will cut there every time - phage binds to specific spot
-Generalized: phage will cut in different spots. non-specific

56
Q

Transduction

A

Cell and phage gene transfer

57
Q

Competent Cell

A

Ability to accept DNA
A cell can be made competent by heat, Calcium chloride chemicals, electroporation (making holes in cell wall)

58
Q

Transformation

A

Cell freely uptakes DNA from environment

59
Q

Conjugation

A

Cell to Cell contact: Conjugation bridge
F-Plasmid, Hfr Strain, donor cell, recipient cell
-pilus V brings cells together then conjugation bridge forms between cells

BIOL (5 decks)

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