Final Exam Lec16-19 Flashcards Preview

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Flashcards in Final Exam Lec16-19 Deck (97):
1

What is the role of Edeine

Binds to small ribosomal unit to block P site

2

How does in vitro transcription and translation work

all necessary RNA polymerase, ribosomes, tRNAs, translation factors are isolated in a tube, just add DNA and protein is produced

3

in bacterial mrnas, degradation is initiated by what?

an endonuclease, usually RNase E

4

What inhibits RNase E activity

a 5' triphosphate

5

What do stem-loop structures do

inhibit exonucleases

6

what helps degradation as bacterial mrnas are deconstructued

3' poly(A) tract

7

can endonuclease activity initiate degredation in eukaryotes?

yes

8

what is the first step in RNA degredation in eukaryotes

poly(a) tail shortening by a deadenylase

9

do 3' poly(A) tails hinder or aid degredation in eukaryotes

hinder

10

what do decapping enzymes do

remove the 5'cap

11

What is viral 'highjacking' of translation

viral mrnas develop ways to compete for translation

12

how do mrnas hijack translation

shut down translation of host mRNAs to hoard resources

13

what is an example of viral hijacking

piconaviruses that cleave translation factors, flu viruses remove the 5' xcap

14

what is the role of picornavirsues

inhibit cap-dependent tranlsation, so themselves use cap-independant tranlsation by isng EREs within the 5' UTR to directly recruit ribosomes

15

what to rotaviruses lack

a 3' poly(A) tail

16

What do Viral mRNAs do to elimate the need to use hostprotein factors

make a closed loop complex via RNA-RNA interactions

17

what are the three main principles of regulatory RNAs

1. to yield the molecule
2. employ complementary base pairing wtih DNA/RNA targets
3. interact with other components (like proteins) to carry out their functions

18

how do regulatory RNAs identify their targets

through base pairing

19

what are the three ways regulatory RNAs can be encoded

1. on the dna strand antisense to the target
2. in a separate DNA region (trans)
3. as part of the target (cis)

20

how long are sRNAs usually

100-300 nt

21

how are most sRNAs encoded

most encoded in trans

22

where to sRNAs usually bind

close to the Shine-Delgarno motif

23

how do some sRNAs affect degredation

by recruiting ribonucleases to the target

24

What happens to RyhB when iron levels are low

ribosomes are prevented from binding, RyhB recruits Rnase E and the mRNA is degraded

25

T or F: sRNAs can interact with multiple targets

T

26

What kind of protein is Hfq

chaperone protein

27

What is the role of the chaperone protein Hfq

a hexameric protein that helps sRNAs find their targets

28

Wha thappens when Hfq levels in a cell are low

sRNAs compete for Hfq and it becomes part of the regulatory system

29

High chitosugar levels induce what

transcription of a 'decoy mRNA'

30

T or F: regulatory RNAs are the same in eukaryotes vs bacteria

true

31

are eukaryotic sRNAs longer or shorter than bacterial sRNAs

shorter

32

what are the three classes of eukaryotic sRNAs

microRNAs (miRNAs)
Small interfering RNAs (siRNAs)
Repeat-associated small interfering RNAs (rasiRNAs)

33

What is argonaute

binds to sRNAs and facilitates their interactions with complementary molecules

34

T or F; All eukaryotic sRNAs carry out their functions in association with Arg

T

35

What are the four Argnaute domains

N, PAZ, Mid and PIWI

36

What does PAZ do

binds the 3' end of bound RNA

37

what does Mid do

interacts with the 5' end of RNA

38

What does PIWI do

related to RNase H and interacts wtih the whole RNA

39

Where are sRNAs dervied from

from different types of long percursor molecules

40

Where are miRNAs derived from

primary transcripts of genes

41

where are si RNAs derived from

double stranded RNAs

42

where are rasiRNAs derived from

repetitive regions of the genome

43

what do processing cuts do

cut precursor RNAs to correct sRNA size

44

What is drosha

relies on accessory protein for positioning and determination of fragment length

45

what is dicer

determines the length of cleaved fragments by securing the 3'of the RNA with the PAZ domain and cutting it

46

what are dicer and drosha

cutting enzymes

47

T or F: several miRNAs can be produced from the same pri-miRNA

True

48

what happens in the microprocessor complex

produces a 60-70 nt hairpin with 3' OH and 5' monophosphate, hairpin exported from the nucleus

49

where are siRNAs derived from

double stranded RNAs from various endo or exogenous sources

50

T are F: siRNAS are involved in clelular defense against exogenous RNAS

true

51

how are MiR:miR* and siR:siR* similar

both have 3'OH and 5' monophosphates
both undergo post-transcriptional modifications such as methylation

52

what is the RISC complex

the guide RNA-Argonaute complex,

53

what does miRISC do

usually pairs initially via 2-8 nucleotide seed sequence, 3' end remains tightly bound by the PAZ domain

54

what doe sthe siRISC do

an bind along its full length, releases PAZ domain and induces conformational change that activates PIWI domain

55

where are miRNA binding sites usually found

in the 3' UTR of the target sequence

56

where does rasiRISCs do

can cleave target RNA, also have epigenetic effects

57

how are foreign nucleic acids removed in eukaryotes

by RNA interference (RNAi)

58

how is viral defence mediated in bacteria

CRISPR

59

how does CRISPR work

contains 20-50 nucleotieds, cleaved foreign DNA cleaved, transcribed by Cas proteins to give short crRNAs

60

What does dicer do

cleaves long dsRNA into short siRNA

61

what does RISC do

RNA-induced silencing complex (includes argonaute)

62

What is the purpose of CRISPR/Cas9

modification of HBB gene, rsponsible for Beta-thalassemia in embryos

63

t or f: sRNAS are larger and more complex than regulatory RNAs

Fals

64

What can riboswitches control

transcription, translation and RNA splicing

65

T or F: riboswitches adopt complex 3D configuration

T

66

Protein binding RNAs can act as _____ to bring proteins into close proximity with one another

tethers

67

What are the three things that regulatory RNAs can bind to in order to exert effects

Other RNAs, Metabolites (Riboswitches), and Proteins (Chaperones, Endonucleases)

68

What is PKU?

phenylketonuria, cannot metabolize phenylalanine and if consumed, mental retardation and ill helath results, genetic disorder, normally Phe converted to Tyr

69

what are SNPs and what do they do

single nucleotide polymorphisms, used as markers for genomic analysis of human diseases

70

what are microsattelites

can be used as genetic markers

71

what is classic mapping

identifies marker all over a genome correlates marker with trait of interest

72

T or F: SNPs and microsattelites are usually the cause of the rare disease under investigation

F

73

What are SNP chips

used to detect SNPs at specific genomic loci

74

recombination tends to take place in "___ ____"

"hot spots"

75

What are the two ways of finding the cause of disease

linkage analysis and association studies

76

What is linkage anaysis

Traces specific disease alleles within families

77

what are association studies

identify disease genes by studying large groups of unrelated individuals,

78

what is the common disease-common variant hypothesis

if a disease is common in a population, there will be a small number of allele for the gene that causes the disease

79

T or F; whole genome sequencing is initally focused on the exome

true

80

What is Pharmacogenomics

uses information from individual genomes to identify treatments that are more likely to be effective on certain individuals

81

what is the difference between gain of function and loss of function genetic causes

Loss of function is a lack of gene expression, while gain of function causes an expression of a gene that causes a disease phenotype

82

What are some of the pros and cons of chain termination dedeoxynucleotide sequencing

Pros:
-Highly accurate
-Widely avaliable
-Short time
-Cost manageable
Cons:
-expensive for fluorescent ddNTPS
-requires a primer

83

What is Illumina dye sequencing

technique used to determine the series of base pairs in DNA , slide flooded with florescently labeled nucleotides

84

what are some of the pros and cosn of Illumina sequencing

Pros:
-Highly accurate
-lower cost
Cons:
-short sequences obtained that must be analyzed computationally

85

whats the difference ebtween a transition and transversion mutatoion

transition occurs if a purine is replaced by other purine or vice versa, whereas a transversion is a purine to a pyrimidine

86

what is dna damage often caused by

cell metabolites

87

T or F; DNA damage can occur from intra and extracellular agents

true

88

UV light promotes what?

pyrimidine dimers

89

what is an example of single point damage

depurination/depyrimidation

90

What is a mismatch repair

fixes mistakes made during replication, using the other strand as a template

91

what are the steps in a mismatch repairq

1. mismatch recognized by MutH
2. MutSLH complex assembles
3. MutH nicks the new strand
4. Nicked strand is digested by exonuclease
5. DNA resynthesized

92

what can repetitive regions of DNA form

hairpins, and can be skipped during replication

93

what protein orchestrates apoptosis (cell death)

protein p53

94

how does protein p53 control cell death

by binding at promoters of target genes to increase proteins that inhibit the cell cycle or stimulate apoptosis

95

T or F: p53 is highly regulated

T

96

how does p53 function when no DNA damage is present

Whne no DNA damage is present, MDM2 ubiquitinates lysines in p53 C-terminal domain, targeting it for degredation

97

how does p53 function when DNA damage is present

kinase activity stimulated and results in phosphoyrilation of p53 and MDM2 so they no longer interact, p53 tetramerizes and interacts with transcription proteins, which acetylates histones and p53