Epigenetics and Translation

Question 1

name 3 mechanisms for epigenetic alterations

Answer 1

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

Question 2

describe DNA methylation

Answer 2

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

Question 3

what are DNMT1 and DNMT3

Answer 3

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

Question 4

describe histone modification

Answer 4

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

Question 5

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

Answer 5

histone acetyl transferase, histone deacetylatase, histone methyl transferase

Question 6

what is chromatin remodeling?

Answer 6

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

Question 7

describe x-chromosome inactivation

Answer 7

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

Question 8

Xist gene

Answer 8

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

Question 9

genomic imprinting

Answer 9

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

Question 10

prader willi syndrome

Answer 10

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

Question 11

gene program

Answer 11

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

Question 12

epigenetic cancer

Answer 12

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

Question 13

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

Answer 13

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

Question 14

describe what happens to the mRNA during translation initiation

Answer 14

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

Question 15

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

Answer 15

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

Question 16

describe elongation

Answer 16

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

Question 17

how does termination occur?

Answer 17

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.

Question 18

peptidyl transferase

Answer 18

forms the new peptide bonds during elongation

Question 19

what is global regulation and what are two mechanisms?

Answer 19

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

1. eIF2
2. eIF4-E

Question 20

describe eIF2 regulation

Answer 20

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

Question 21

describe the availability mechanism of eIF4E regulation

Answer 21

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

Question 22

how does Rapamycin work

Answer 22

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

Question 23

describe phosphorylation mechanism of eIF4E regulation

Answer 23

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

Question 24

what is MNK1 and protein kinase C

Answer 24

they phosphorylate serine 209 on eIF4E, increasing translation

Question 25

describe the iron example of local regulation

Answer 25

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

Question 26

at what level is local translation regulation

Answer 26

mRNA stability

Question 27

describe how miRNA can regulate mRNA

Answer 27

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

Question 28

what is Drosha?

Answer 28

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

Question 29

what is the Dicer/R2D2 complex?

Answer 29

cleaves pre-miRNA into miRNA

Question 30

epigenetics

Answer 30

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