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Bacteriology > Chapter 8 > Flashcards

Chapter 8 Flashcards

1
Q

transcription

A
  • Reading a DNA template to make an RNA copy
  • RNA transcripts complementary to the DNA template strand
  • carried outa by a complex enzyme, RNA polymerase
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2
Q

translation

A

Decoding mRNA to assemble protein

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3
Q

Gene expression

A

After translation, each polypeptide must be properly folded and placed at the correct cellular or extracellular location

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4
Q

RNA polymerase holoenzyme is composed of

A

Core polymerase
-Required for the elongation phase

Sigma factor

  • Required for the initiation phase
  • helps the core enzyme detect promoters
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5
Q

“housekeeping” sigma factor

A
  • In E. coli, it is sigma-70.

- Recognizes consensus sequences at the –10 and –35 positions, relative to the start of the RNA transcript (+1)

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6
Q

Transcription occurs in three phases

A
  1. Initiation
    - RNA polymerase holoenzyme binds to the promoter
    - This is followed by melting of the helix and synthesis of the first nucleotide of the RNA
  2. Elongation
    - the RNA chain is extended
  3. Termination
    - RNA polymerase detaches from the DNA and releases the transcript
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7
Q

two transcription termination signals

A
  1. Rho-dependent
    Relies on a protein called Rho and a strong pause site at the 3′ end of the gene after the stop codon
  2. Rho-independent
    Requires a GC-rich region of RNA that forms a hairpin structure, as well as 4–8 consecutive U residues
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8
Q

Different Classes of RNA

A
  • Messenger RNA (mRNA): encodes proteins
  • Ribosomal RNA (rRNA): forms ribosomes
  • Transfer RNA (tRNA): shuttles amino acids
  • Small RNA (sRNA): regulates transcription or translation
  • tmRNA: frees ribosomes stuck on damaged mRNA
  • Catalytic RNA: carries out enzymatic reactions, e.g., rRNA
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9
Q

nucleotide triplets

A

-64 possible codons
-61 specify amino acids
Include the start codon(s)
-3 are stop codons
-Multiple codons can encode the same amino acid
-operates universally across species

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10
Q

tRNA Molecules

A
  • convert the language of RNA into that of proteins
  • Anticodon: hydrogen bonds with the mRNA codon specifying an amino acid
  • 3′ (acceptor) end: binds the amino acid
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11
Q

Attaching Amino Acids to tRNA

A
  • Each tRNA must be charged with the proper amino acid before it encounters the ribosome
  • carried out by a set of enzymes called aminoacyl-tRNA synthetases
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12
Q

Ribosome

A
  • composed of two subunits, each of which includes rRNA and proteins
  • subunits are 30S and 50S and combine to form the 70S ribosome
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13
Q

70S ribosome harbors three binding sites for tRNA

A
  1. A (acceptor) site: binds incoming aminoacyl-tRNA
  2. P (peptidyl-tRNA) site: harbors the tRNA with the growing polypeptide chain
  3. E (exit) site: binds a tRNA recently stripped of its polypeptide
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14
Q

peptidyltransferase

A
  • actually a ribozyme

- makes the peptide bonds that stitch amino acids together

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15
Q

Shine-Dalgarno sequence

A

ribosome-binding site

-is complementary to a sequence at the 3′ end of 16S rRNA of the 30S subunit

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16
Q

Three Stages of Protein Synthesis

A
  1. Initiation: brings the two ribosomal subunits together, placing the first amino acid in position
  2. Elongation: sequentially adds amino acids as directed by the mRNA transcript
  3. Termination: releases the completed polypeptide and the ribosomal subunits
17
Q

Antibiotics That Affect Translation

A
  • Streptomycin

- Tetracycline

18
Q

coupled transcription and translation

A
  • Different ribosomes can be translating each gene within a polycistronic mRNA.
  • Before RNA polymerase has even finished making an mRNA molecule, ribosomes will bind to the 5′ end of the mRNA and begin translating protein
19
Q

Protein structure may be modified after translation

A
  • Phosphate and other groups can be attached
  • Sugars can be attached to make glycoproteins
  • Lipids can be attached to make lipoproteins
  • Proteolytic cleavages may occur
20
Q

Protein Folding

A

-Folding of many proteins requires assistance from other proteins called chaperones

21
Q

Proteasomes

A

-protein-degrading machines found in eukaryotes and archaea

22
Q

Protein Degradation

A
  • proteins have a half-life

- Bacteria contain ATP-dependent proteases

23
Q

Proteins destined for the bacterial cell membrane

A
  • require special export systems.
  • tagged with hydrophobic N-terminal signal sequences of 15–30 amino acids.
  • sequences are bound by the signal recognition particle (SRP)
  • Proteins then undergo cotranslational export
24
Q

periplasmic proteins

A
  • in gram negative cells
  • maltose-binding protein
  • delivered to the periplasm by a common pathway called the SecA-dependent general secretion pathway
25
Q

Journeys through the Outer Membrane

A
  • Seven secretion systems have evolved
  • Type I protein secretion moves certain proteins directly from the cytoplasm to the extracellular environment.
  • An efflux ABC transporter
  • Uses TolC channel
  • one thing that is secreted is hemolysin which damages red blood cells
26
Q

Bioinformatics

A
  • the computerized study of DNA sequences

- Data enable scientists to make predictions about an organism’s physiology and evolution

27
Q

Annotation

A
  • labeling of the DNA sequence functions
  • Computers look for patterns, such as regulatory sequences, promoters, open-reading frames (ORFs), and rRNA and tRNA genes
28
Q

open-reading frames (ORFs)

A
  • is a sequence of DNA that encodes a polypeptide

- Begins with start codon and ends with stop codon

29
Q

Orthologous genes (orthologs)

A
  • Homologous genes in different species
  • Have same function in different organisms
  • Over time can diverge to have different functions
30
Q

Paralogous genes (paralogs)

A
  • Genes duplicated and then diverge within a species.

- Have slightly different functions (depends of degree of divergence)

31
Q

homologous (homologs)

A
  • evolved from a common ancestral gene
    Two kinds:
    1. Orthologous genes, orthologs
    2. Paralogous genes, paralogs

Bacteriology (16 decks)

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