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Biochem 2 > Epigenetics and Translation > Flashcards

Epigenetics and Translation Flashcards

1
Q

name 3 mechanisms for epigenetic alterations

A
  1. DNA methylation
  2. Histone modifcation
  3. Chromatin remodeling complex
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2
Q

describe DNA methylation

A

DNA methylation is associated with repression. Approx. 70% of CpGs are methylated.
de novo methylation- DNMT3. creates hemimethylation (only one side of DNA is methylated)
maintenance methylation- DNMT1 methylate hemimethylated pairs

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3
Q

what are DNMT1 and DNMT3

A

they are DNA methyltransferases. DNMT1 codes for maintenance enzymes whereas DNMT3 codes for de novo enzymes

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4
Q

describe histone modification

A

primarily refers to acetylation and methylation. acetylation occurs lysine side chains in the histone subunits are acetylated by histone actyl transferase (HAT). They are deactylated by histone deacetylatases (HDACs). methylation attaches methyl groups to lysine and arginine residues in H3/4 N-terminals. both acetylation and methylation are associated with activation

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5
Q

What do the enzymes HAT, HDAC, and HMT do?

A

histone acetyl transferase, histone deacetylatase, histone methyl transferase

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6
Q

what is chromatin remodeling?

A

a chromatin remodeling complex contains ATPase capable of dissociating histones from DNA for activation

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7
Q

describe x-chromosome inactivation

A

facilitates dosage compensation in females, one x becomes a barr body. deactivation is mitotically inhereted (mosiacs). depends on the x chromosome inactivation center and the Xist gene. Xist region produces RNA coating of inactive x- 1st step

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8
Q

Xist gene

A

found in the chromosome inactivation center of the inactive x chromosome, it results in RNA coverage of the inactive X as the first step in barr body formation

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9
Q

genomic imprinting

A

“imprinting” refers to the epigenetic inactivation of genes that is passed down from maternal or paternal sources. Imprinting occurs during gametogenesis.

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10
Q

prader willi syndrome

A

maternal copy of genes on chromosome 15 imprinted, paternal non functional

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11
Q

gene program

A

epigenetic regulation is important for gene expression in specific tissue subsets that need specific gene activation

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12
Q

epigenetic cancer

A

can be caused by poor epigenetic regulation with no error in the genetic code itself

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13
Q

describe the first steps in initiating the 40S subunit for translation

A

40S subunit has eIF3 and 1a bound. It then binds the terenary unit which contains the tRNAmet/eIF2/GTP. 40S also binds eIF1 and eIF5

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14
Q

describe what happens to the mRNA during translation initiation

A

initiation factors recognize the 7-methylguanasine 5’ cap. the eIF4 complex binds (eIF4E, F, G, A). The eIF4b uses ATP to unwind the mRNA. The mRNA is then ready to join the 40S subunit

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15
Q

describe what happens after the 40S subunit and the mRNA have joined

A

the 40S subunit uses ATP to scan for start codon. Once the start codon is found, the GTP of the terenary unit is cleaved (along with eIF2), and eIF5b uses GTP to disassociate the remaining translation units. the large subunit then binds and translation begins

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16
Q

describe elongation

A
  1. tRNAmet is in the P site
  2. EF-Tu bring next tRNA into the A site
  3. peptide bond is formed between P and A sites, requiring GTP
  4. Ribosome move towards 3’ end
  5. Peptide in P site ejected out E site and peptide in A site moves to P site
17
Q

how does termination occur?

A

when a stop codon is read, a release factor binds in the A site whic causes peptidyl transferase to bind water instead of a tRNA.

18
Q

peptidyl transferase

A

forms the new peptide bonds during elongation

19
Q

what is global regulation and what are two mechanisms?

A

global regulation occurs at the level of initiation and affects all protein translation.

  1. eIF2
  2. eIF4-E
20
Q

describe eIF2 regulation

A

eIF2 is important for promoting the binding of tRNAmet to the start codon. after it stabilizes the rRNA/start codon, it disassociates via GTP hydrolysis, leaving it with only GDP. It must have GTP to do its job, and so GTP is rephosphorylated by eIF2B. If eIF2 is phosphorylated, then it binds too tightly to eIF2B and GDP cannot be phosphorylated

21
Q

describe the availability mechanism of eIF4E regulation

A

eIF4E binds to the 5’ cap of mRNA and promotes binding of 40S unit. when not in use, 4E is bound by 4E-BP. it is released when 4E-BP is phosphorylated. mTOR/raptor/LST8 complex phosphorylates 4E-BP, and it monitors the environment for optimal translation conditions

22
Q

how does Rapamycin work

A

it inhibits mTOR, thereby preventing translation, (in this case preventing lymphocyte proliferation in transplant patients)

23
Q

describe phosphorylation mechanism of eIF4E regulation

A

phosphorylation of serine 209. Creates a salt bridge that makes a higher affinity bond with mRNA, preventing its disassociation and increasing the affinity for 40S subunit. phosphorylation occurs d/t MNK1 or Protein Kinase C

24
Q

what is MNK1 and protein kinase C

A

they phosphorylate serine 209 on eIF4E, increasing translation

25
Q

describe the iron example of local regulation

A

in times of excess iron, ferritin is upregulated to sequester iron inside cells and transferrin is down regulated to prevent more uptake. vice versa under starvation. each of their mRNA sequences have a stem-loop called Iron Response Element. Under starvation, cytosolic aconitase binds to these loops, activating transferrin and down regulating ferritin. It unbinds during excess iron (when it binds iron itself), upregulating ferritin and down regulating transferrin

26
Q

at what level is local translation regulation

A

mRNA stability

27
Q

describe how miRNA can regulate mRNA

A

can be coded for as an intron or separately. gets processed with tail/cap etc. forms a 3-D structure that specifies it for transportation to nucleus. RNase containing Drosha protein cleaves pri-miRNA into a ~70nt sequence w/ imperfect loop called pre-miRNA. exported to cytosol where it is cleaved again by Dicer/R2D2 into a 22nt. it associates into the RISC complex, providing the specificity. when RISC binds, if the miRNA is complementary, the mRNA will be destroyed

28
Q

what is Drosha?

A

found in the nucleus, associated with the RNase that cleaves pri-miRNA into pre-miRNA

29
Q

what is the Dicer/R2D2 complex?

A

cleaves pre-miRNA into miRNA

30
Q

epigenetics

A

differences in phenotype but not related to changes in genotype. changes are maintained thru mitosis but are reversible and primarily related to chromatin remodeling

Biochem 2 (4 decks)

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