Molecular biochemistry W10

Question 1

Where does Noncoding RNAs serve as intermediates

Answer 1

In the central dogma

Question 2

what is rRNA and tRNA essential for

Answer 2

• Protein synthesis

Question 3

What does telomerase RNA serve as a template fro

Answer 3

• Serves as a template for telomere replication

Question 4

WHt does snoRNAs modify

Answer 4

They modify ribosomal RNA

Question 5

What does is snRNA important in

Answer 5

RNA splicing

Question 6

What does Xist RNA inactivate

Answer 6

One X chromosome in females

Question 7

What is the function of ncRNAs

Answer 7

• Help regualte gene expression and
• protect the genome from virsues and transposons

Question 8

Explain how short ncRNAS function in RNA interference (RNAi)
-what they act as
-what they bind and what this leads to

Answer 8

• Short ncRNAs act as guide RNAs.

They bind to specific mRNAs by base-pairing, leading to:

Translation inhibition.

mRNA degradation.

Chromatin remodeling

Question 9

Name the 3 key types of small noncoding RNAs

Answer 9

• miRNAs( microRNAs)
  -siRNAs(small interfering RNA)
• piRNAs( piwi interacting RNAs)

Question 10

What is miRNAs- microRNAs synthesized by

Answer 10

• RNA polymerase 2

Question 11

What does miRNAs regulate

Answer 11

Regulate translation and stability of at least one third protein coding genes

Question 12

What is miRNA incorporated into

Answer 12

RISC( RNA- induced silencing complex) which targets mRNA via base pairing

Question 13

What does siRNAs and PiRNAs reduce

Answer 13

Gene expression

Question 14

Name a protein that is part of the RISC + function

Answer 14

• Argonaute, It positions the 5’ region of miRNA for base-pairing with target RNA

Question 15

What is the advantages of miRNAs

Answer 15

• A single miRNA can regulate many mRNAs sharing common seqeuence
• miRNAs are small but impactful, therfore effiecnt use of genome space

Question 16

Explain what is combinatorial control in relation to miRNAs

Answer 16

• Where multiple miRNAs can target the same mRNA, increasing repression

Question 17

What else does miRNA function in

Answer 17

Defense by degrading foreign dsRNA from viruses or transposons

Question 18

Explain the evolutionary perspective of siRNAs and miRNAs

Answer 18

siRNAS- acient and widespread
miRNAS- evoolved later as refinement

Question 19

Name the compoentns that form the RITS complex(RNA - induced transcriptional silencing)

Answer 19

• siRNAS+ Argonaute+ other proteins form the RITS complex

Question 20

What does the RITS complex bind + recruit + what does this binding and recruting lead to

Answer 20

• Binds nascent RNA transcripts
  and recruits chromatin-modifying proteins
  This leads to :
• Histone modifications
  -Heterochromatin formation
  -Gene silencing

Question 21

What happens in the positive feedback loop in relaltion to RITS complex- what does it recruit and whay

Answer 21

• It recruits RNA dependent RNA polymerase and dicer to sustain siRNA production

Question 22

What are the functions of positive feedback loop in RITS

Answer 22

• Silencing of transposable elements
  -Maintenance of centromeric heterochromatin for chromosome segregation during mitosis

Question 23

What is the primary role of piwi -interacting RNAs( piRNAs)

Answer 23

To silence transposable elements

Question 24

Compare piRNAs to miRNAS /siRNAs

Answer 24

• They are longer then miRNAs/siRNAs
  -Do not require Dicer enzyme for processing

Question 25

What are piRNAs associated with

Answer 25

Associated with Piwi proteins

Question 26

What are piRNAs transcribed from

Answer 26

Transcribed from genomic clusters of transposon sequemce fragments

Question 27

What are piRNAs processed into

Answer 27

- short single strands

Question 28

What do scientists use RNAi for

Answer 28

To inactivate specific genes in cultured cells

Question 29

What medical use could RNAi have

Answer 29

In gene therapy

Question 30

What is RNAi used by cells for

Answer 30

For gene regulation and chromosome structure maintenance

Question 31

What does RNAi stand for

Answer 31

RNA interference

Question 32

What does bacteria and aracheae used to protect against viral infectiosn

Answer 32

CRISPR systems

Question 33

Name the 3 key steps of the CRISPR system

Answer 33

-Integration -Transcription -Targeting

Question 34

Explain what happens in the integration step in the CRISPR mechanism

Answer 34

- Fragments of viral DNA are inserted into CRISPR loci in the host genome, forming a genetic memory

Question 35

Explain what happens in the transcription step in the CRISPR systems

Answer 35

- The loci are transcribed into long RNAs and processed into crRNAs( CRISPR RNAs)

Question 36

What happens in targeting steps

Answer 36

crRNAs asscoiate with CAS proteina to seek out and destroy mathcing vira double stranded DNA

Question 37

What is the CRISPR system also similar to and how

Answer 37

Adaptive immunity: as it remembers and targets previosuly encountered viruses

Question 38

What are CAS proteins functionally similar to + what have they been engineered for

Answer 38

- Argonaute proteins+ piwi proteins -Engineered for genome editing in plants and animals

Question 39

What does IncRNAs stand for

Answer 39

Long NONcoding RNAs

Question 40

What is lncRNA transcribed by

Answer 40

RNA polymerase 2

Question 41

Name 2 unifying functional mechanism of lncRNA

Answer 41

1. Scaffold function 2. Guide function

Question 42

What happes in scaffold function+ what does the structure allow

Answer 42

- lncRNA bring proteins together to coordinate their actions -The structure allos them to bind to various proteins

Question 43

What happens in guide function

Answer 43

lncRNA binds to DNA or RNA via base pairing to guide proteins to specific sequences

Question 44

IncRNA similar to the guide function of what

Answer 44

- similar to the guide function of miRNAs, crRNAs and snoRNAs

Question 45

What does Antisense IncRNAs transcribe + WHY DO THEY Bind to mRNAs

Answer 45

- They transcribe opposite protein coding genes - Bind to mRNAs to block translation or alter splicing

Question 46

What do sponge IncRNAs bind to + effect

Answer 46

Bind to miRNAs and inhibit their function

Question 47

What can some IncRNAs be

Answer 47

- Cytoplasmic or nuclear (which is the well understood ones)

Question 48

What does RNAi use to regulate mRNA and gene expression

Answer 48

Uses miRNA, siRNA and piRNA

Question 49

What are piRNAs involved in + and where do they specifically work

Answer 49

- Involed in RNA interference -Work specifically in the germ line

Question 50

Name the 2 base pairing outcomes in miRNA targeting using RISC

Answer 50

- Extensive pairing -Partial pairing

Question 51

Which type of base pair outcome is common in humans in mRNA targeting via RISC

Answer 51

Partial pairing

Question 52

In extensive pairing ( a base pairing outcome) explain what happens starting with mRNA

Answer 52

- mRNA is cleaved by Argonaute, which leads to degredation -RISC is then released to cleave more mRNAs

Question 53

In partial pairing( a base pairing outcome) what is repressed + where is mRNA sent

Answer 53

- Translation is repressed -mRNA is sent ti P-bodies,

Question 54

Explain the mechanism of RNAi as a cell defense mechanism starting with a DICER.

Answer 54

- Dicer cleaves dsRNA into siRNA -siRNA binds to RISC -Argonaute cleaves the target RNA , causing degredation -RNAi can spread between cells for systemic defense