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Molecular biology (Updated 2016) > 01 Protein Synthesis, Antibiotics, and Prion Diseases > Flashcards

01 Protein Synthesis, Antibiotics, and Prion Diseases Flashcards

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1
Q

what came first DNA or protein?

A

neither RNA was first

*evidence is derived primarily from the ability of RNA to catalyze RNA reactions. RNA has the beginnings of catalytic ability to self-replicate and to produce protein.

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2
Q

central dogma of molecular biology

A

sequence of information flows from DNA to RNA to Protein

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3
Q

What are the main steps of protein synthesis that can be regulated in eukaryotes?

A

1) transcription
2) processing of hnRNA
3) translation
4) ribosomal protein synthesis

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4
Q

What is the process of transcription?

A

the process wherein sequence information contained in the chromosomal DNA molecule is used to make a complementary RNA copy of the original DNA sequence

depends on interplay of several key sequence elements (ex 3’/5’ UTR, promoter, enhancer, etc)

carried out by RNA Polymerase

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5
Q

What are the features of monocistronic transcription in eukaryotes?

A
  • 5’ UTR & 3’ UTR
  • introns are removed / exons are expressed
  • 5’ 7mGppp cap and 3’ poly-A tail are added to mature mRNA
  • mature mRNA is no longer co-linear with genomic DNA
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6
Q

promoter

A

5’ to coding region; sequece that is responsible for assembly of RNA Pol complex and intiation of transcription

sequence elements responsible for recognition by DNA-binding proteins (transcription factors, RNA pol II, associated components) regulating that gene; may be facilitated by an enhancer element or enhancer RNA

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7
Q

enhancer element or enhancer RNA

A

chromosomal sequences responsible for up-regulating the activity of an associated promoter

may function in either orientation, and may be upstream, downstream, or even embedded within an intro of the gene being regulated

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8
Q

transcription start site

A

the point in a DNA sequence at which transcription of a gene into RNA begins (NOT the start codon)

prokaryotes - consensus sequence
eukaryotes - defined by transcription factors

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9
Q

terminator

A

the point in a DNA sequence at which transcription of a gene into RNA ceases
(NOT the stop codon)

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10
Q

What are some of the products of transcription?

A

most RNA transcribed is mRNA, but the bulk of total RNA is tRNAs, rRNAs, and other ncRNAs

> 50% is hnRNA = precursors to mRNA
most cellular RNA is rRNA or tRNAs

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11
Q

What are the main steps of transcript maturation in eukaryotes?

A

eukaryotic mRNAs must undergo multistep processing to become mature RNA

  • addition of a 3’oriented 7-methylG-PPP cap at the 5’end
  • polyadenylation
  • splicing of introns on spliceosomes
  • association with intra-nucelar transport proteins
  • export to the cytoplasm
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12
Q

When can expression of the transcript be affected?

A

at any point in the transcription process

the amount of mRNA transcripts present does NOT correlate with the amount of protein being expressed or translated (**clinically relevant)

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13
Q

RNA Pol III

A

5S rRNA and tRNA

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14
Q

processing of hnRNA

A

during transcription, in eukaryotes, produces mature mRNA via multiple steps (addition of 5’ cap and 3’ Poly-A tail)

in prokaryotes the primary transcript of can usually function as the mRNA

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15
Q

translation

A

the act of physically polymerizing amino acids together in a specific sequence dictated by the mRNA

multiple steps and high energy process

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16
Q

mRNA characteristics

A

made abundantly in the cell but has rapid turnover

> 50% is hnRNA = precursors to mRNA
<3-5% of cell’s RNA is mature mRNA

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17
Q

How is translation initiated?

A

1) RNA captures small ribosomal subunit at the ribosome binding site (prokaryotes) or at the 5’ end of the mRNA (eukaryotes)
2) large subunit is captured
3) translation initiation factor binds to the P site at met codon
* *requires that tRNA anticodon basepair with mRNA codon

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18
Q

Universal Genetic Code

A

The standard codon usage that is common to most organisms

**be able to use this table FINAL EXAM QUESTION
INSERT IMAGE OF TABLE or see notes

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19
Q

How does the polypeptide grow?

A

1) elongation factor (EF), complexed with an aminoacyl-tRNA and GTP, loads onto the “A site”
2) 1 GTP is hydrolyzed to release EF
3) peptidlytransferase activity (RNA-catalyzed) created peptide bond and translocated peptide to the “P site”, with hydrolysis of 1 GTP

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20
Q

How much energy is used to grow the polypeptide?

A

formation of 1 peptide bond requires expenditure of 4 high energy PO4 bonds

  • 2 released when loading aa onto tRNA
  • 1 released when freeing the elongation factor
  • 1 released during peptide translocation
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21
Q

Cachexia

A

may occur in conditions involving rapid cellular proliferation or greatly enhanced metabolism
results in the degradation and loss of normal tissue (wasting, patients metabolize their own tissues)
ex:
- patients with large or widely metastasized tumors
- individuals with severe malaria (due to elevated TNFα)

22
Q

antibiotics

A

many currently in use exert their action by affecting protein synthesis at various points in the process of translation

differences is the process between eukaryotics and prokaryotics may affect their function

23
Q

chloramphenicol

A

affects prokaryotes
blocks the peptidyl transferase reactions

can also affect organellar protein synthesis in eukaryotes

24
Q

erthromycin

A

affects prokaryotes

blocks the translocation of the peptidyl-tRNA from the A site to the P-site

25
Q

rifamycin

A

affects prokaryotes

inhibits RNA polymerase

26
Q

tetracyclines

A

affects prokaryotes

blocks binding of aminoacyl-tRNA to the A site of the ribosome

27
Q

antibiotics

A

many currently in use exert their action by affecting protein synthesis at various points in the process of translation (NOT all antibiotics block protein synthesis)

differences is the process between eukaryotics and prokaryotics may affect their function

28
Q

What antibiotics affect the translation process in eukaryotes?

A

anisomycin
cycloheximide
α-amantin

puromycin
actinomycin D

29
Q

anisomycin

A

affects eukaryotes

blocks the peptidyl transferase reaction of cytoplasmic ribosomes

30
Q

cycloheximide

A

affects eukaryotes

blocks translocation of peptidyl-tRNA from the A site to the P site on the ribosome

31
Q

α-amantin

A

affects eukaryotes

inhibits RNA polymerase II

32
Q

puromycin

A

affects both prokaryotes and eukaryotes

imitates aminoacyl-tRNA. becomes covalently bound to the growing end of the peptide chain to terminate translation

33
Q

actinomycin D

A

affects both prokaryotes and eukaryotes

binds to DNA, preventing transcription

34
Q

α-amantin

A

affects eukaryotes
inhibits RNA polymerase II

made by Amantia muscaria (mushroom)
highly hepatoxic > liver failure > liver transplant
easily lethal

35
Q

How are antibiotics used to fight malaria?

A

antibiotics are used to BLOCK protein processing

targets the 2nd cleavage (PEXEL) to prevent export of the protein to the RBC cell membrane

malaria, small protozoa parasite, eukaryotic, live in RBC

36
Q

α-amantin

A

affects eukaryotes
inhibits RNA polymerase II

made by Amantia muscaria (mushroom)
highly hepatoxic > liver failure > liver transplant
easily lethal

37
Q

When can antibiotics block protein synthesis?

A

at ANY point in the process
anywhere the host & pathogen differ biologically

  • some antibiotics are highly effective but NOT clinically useful (ex: α-amantin)
  • depending on the microorganism there are novel points in the expression of proteins that remain to be effectively targeted (ex: malaria)
38
Q

Primary protein structure

A

linear sequences of amino acids

39
Q

secondary protein structure

A

simple fold, coils, etc made of primary structure

ex: α-helix, β-sheet

40
Q

tertiary protein structure

A

complex overall conformation made up of of multiple primary and secondary structures

may require prosthetic groups to complete structure

41
Q

quaternary protein stucture

A

multi-subunit associations of apoproteins (subunits) to make holoprotein (complete, functional protein)

ex: hemoglobin has 4 subunits

42
Q

mechanism of folding the polypeptide

A

molecules can rotate about any unrestrained bonds

  • allows a large molecule to assume a massive number of possible conformations
  • proteins are functional in only very small, finite # of conformations
  • proline - cannot rotate, restrained by its conformation

growing polypeptide will always seek the lowest energy state. Often this is NOT functional. Requires chaperonins

43
Q

chaperonin mechanism

A

1) chaperonin accepts unfolded/partially folded polypeptide
2) sequesters polypeptide away from other proteins to prevent aggregation
3) chaperonin undergoes conformational changes to help drive folding
* energy expensive process

44
Q

What are some TSE’s?

Transmissible Spongiform Enchephalopathies

A
  • first observed in sheep - Scrapie
  • recently bovine spongiform encephalopathy (BSE)
    crossed over into human population has generated a new variant Creutzfeld-Jacob Disease (nvCJD)
  • first found to be transmissible with Kuru passed by ritualistic cannibalism
45
Q

scrapie

A

in sheep, neurologic disease
exhibit behavioral changes, loss of herding, uncoordinated movement, bunny hopping gain,
advanced cases by exhibit “scraping” behavior with loss of wool

46
Q

How does one contract a TSE? How transmissible are they?

A
  • ingestion of contaminated foods, including via cannibalism
  • grafts, esp. dura mater
  • blood transfusion
  • NOT by casual or sexual contact

fairly transmissible; have been found across species, contaminated ground, plant leaves

47
Q

What are the characteristics of a TSE?

A

prion; Transmissible Spongiform Enchephalopathies
- diseases is essentially the end result of self-perpetuating inappropriate chaperone-like activity
- all are thought to involve autocatlytic conversion of PrPc protein to PrPsc
(same protein ortholog in all species of mammals)
- in the refolding process some of the α-helical regions in PrPc unfold forming an extended β-sheet region

48
Q

PrPc

A 
normal protein (in TSE but normally in body)
may be involved in long term memory
has a lot of α-helical folding; very little β-sheet folding

*same primary structure as PrPsc different higher structures

49
Q

PrPsc

A

abnormal protein in TSE
~40% β-sheet; decreased α-helical folding
does not degrade and accumulate in the brain; different sources of prions cause different patterns of accumulation

*same primary structure as PrPsc different higher structures

50
Q

diagnostic tests for TSE

A

detection via IQ-RT-PCR; immunoquantitative real time PCR
a combination of ELISA followed by PCR

takes advantage of the autocatalytic function of prions to enhance sensistivity

51
Q

Can TSE’s be treated?

A

promising evidence for 4 different approaches
limited by the blood brain barrier

most clinically promising is Anti-PrPc shRNA

  • transcribed by lentivirus vector
  • reduces Prpc mRNA and biosynthesis
  • folds and forms a hairpin when transcribed
  • *must be injected directly into the brain

Molecular biology (Updated 2016) (15 decks)

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