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MICRB 265 > Week 9 > Flashcards

Week 9 Flashcards

1
Q

Gene (3 definitions)

A
  • the basic unit of genetic information
  • also defined as the nucleic acid sequence that codes for a polypeptide, tRNA or rRNA
  • linear sequence of nucleotides with a fixed start point and end point
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2
Q

DNA gene structure

A

promoter = has RNA pol binding site
transcription starts -> leader —> trailer —> terminator

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3
Q

mRNA gene structure

A

-leader (has shine-dalgarno sequence where ribosome binds)
-translation starts (start codon) –> stop codon –> trailer

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4
Q

coding strand

A

5’ to 3’

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5
Q

template strand

A

3’ to 5’

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6
Q

Bacteria frequently cluster all of the genes required for ______

A

-formation of a particular structure

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7
Q

Locus (def.)

A

position on a genome (this far from oriC)

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8
Q

Gene cluster (def.)

A

cluster of gene encoding proteins involved in the biosynthesis of one structure

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9
Q

Operon (def.)

A

series of genes contranscribed –> one mRNA for all the genes, same promoter + terminator (can determine by experimentation)

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10
Q

operon produces ____ mRNA (has _____)

A

-polycistronic
-open reading frame for each gene

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11
Q

mRNA matches which strand of DNA expect T/U

A

coding strand (5’ -> 3’)

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12
Q

start codon ? codes for?

A

-AUG
-N-formylmethionine, a modified amino acid used to initiate protein synthesis in bacteria

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13
Q

stop codon ?

A

-UAA, UAG, UGA

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14
Q

stop codon is immediately followed by ______

A

trailer sequence which contains a terminator sequence used to stop transcription

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15
Q

codon (def.) + ______ is complementary

A

-genetic code word, 3 base pairs long, that specifies an amino acid
-anticodon on tRNA

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16
Q

start codon (def.) sense codon? stop (nonsense) codon?

A

-start site for translation
-the 61 codons that specify amino acids
-the three codons used as translation termination signals (do not encode amino acids)

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17
Q

Code degeneracy (def.)

A
  • up to six different codons can code for a single amino acid (61 codons for 20 a.a)
18
Q

Codon usage bias (def.)

A

some of a.a are used more often; fewer tRNA in TRNA pool for some codons; this slows down translation at these sites

19
Q

3rd base pair wobble

A

-3rd base pair of codon is more likely to be unique (loose base pairing)
-eliminate need for unique tRNA for each codon

20
Q

Reading frames

A

-reading frame specifies where the codons are
-ribosome binding site (shine sequence) is always 6-7 bp upstream of the start codon

21
Q

Polymers of amino acids linked by _____

A

-peptide bonds

22
Q

amino acids have _____ (4). a.a can be _____ depending on side chain

A

-central carbon, carboxy group (C-terminal), amino group (N-terminal), side chain
-polar, non-polar, or charged

23
Q

peptides have directionality

A

N -> C

24
Q

Translation initiation

A

1 – binding of mRNA to 30S subunit (mediated by Shine Dalgarno sequence)
2 – binding of initiator tRNA to complex
3 – Hydrolysis of GTP by initiation factors to bring 50S subunit

25
Q

Intact ribosome contains 3 sites:

A
  • A site (amino acid) -> new tRNA
  • P site (peptide) -> peptide is extended (initial tRNA binds here)
  • E site (exit) -> empty tRNA leaves
26
Q

Translation elongation consists of three phases

A
  • aminoacyl-tRNA binding
  • transpeptidation reaction
  • translocation -> whole ribosome moves over one codon
27
Q

Translation elongation involves several ______

A

elongation factors (EFs)

28
Q

Elongation: aminoacyltRNA binding

A

-aminoacyl-tRNA enters ribosome based on codon
-requires EF-Tu and GTP hydrolysis

29
Q

Elongation: transpeptidation

A

-formation of peptide bond
-catalyzed by peptidyl transferase activity of 23S rRNA (ribozyme)
-amino group on the A site amino acid performs nucleophilic attack on the carboxyl group of the Cterminal amino acid on the P site tRNA (peptide bond formation)
-peptide chain transferred from the P site to A site

30
Q

Elongation : translocation (three simultaneous events)

A
  • peptidyl-tRNA moves from A site to P site
  • ribosome moves down one codon
  • empty tRNA moves to E site and dissociates
  • requires EF-G (translocase) and GTP hydrolysis
31
Q

Translation termination

A

-Takes place at any one of three codons (nonsense (stop) codons – UAA, UAG, and UGA)
* Release factors (RFs) -> aid in recognition of stop codons, 3 RFs function in prokaryotes, only 1 RF active in eukaryotes)
* GTP hydrolysis required
* Ribosome dissociates into 30S and 50S components

32
Q

Protein maturation involves 4 things

A
  • Folding
  • Posttranslational modifications
  • Complex formation
  • Localization
33
Q

Chaperone proteins do what? + examples + work by ____

A
  • Help proteins fold properly
    -DnaKJ complex or GroEL-GroES complex
    -excluding water to allow hydrophobic regions to form properly
34
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
35
Q

posttranslational modifications descr. + function

A

-some go on for the life of the protein and some are dynamic
- change the activity, localization, stability, binding partners of a protein

36
Q

posttranslational modifications examples

A
  • acetylation
  • methylation
  • phosphorylation
  • glycosylation
  • uridylylation
  • proteolysis
  • prosthetic group
37
Q

Localization: Sec system

A
  • transports unfolded proteins through membrane and helps integral membrane proteins fold
  • requires an N-terminal signal sequence
  • requires ATP hydrolysis
38
Q

Localization: Tat system

A
  • transports folded proteins through membrane
  • requires an N-terminal signal sequence (twin arginine)
  • requires proton motive force
39
Q

protein with signal sequence + SecA =

A

protein secrted into periplasm

40
Q

protein with signal sequence + signal recognition particle =

A

protein inserted into membrane

41
Q

Secretion systems

A

Type I (ABC transporter) = cytoplasm to outside
Type II (found in most bacteria) =require Sec/TAT; periplasm to outside but extends into cytoplasm; folded proteins
Type V (found in most bacteria) =require Sec/TAT; periplasm to outside; unfolded
Type III: injectisome (proteins), requires ATP, used by pathogenic bacteria (salmonella), injects toxins directly into host cells
Type IV: injectisome (DNA), requires ATP, some secrete proteins, most are type IV pili & transfer DNA
Type VI: retracted sheath -> contracted (needle); secretes proteins directly into other cells as part of bacterial warfare, requires ATP

MICRB 265 (12 decks)

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