Cmcb Rna Synthesis

Front 1

1/5 of all disease alleles affect splicing?

Back 1

True

Front 2

1/5 of all disease alleles affect splicing?

Back 2

True

Front 3

Describe bact transcription translation?

Back 3

occurs simultaneously

Front 4

Describe bact transcription translation?

Back 4

occurs simultaneously

Front 5

Spinal Musclular Atrophy

Back 5

autosomal recessive disease; progressive degenerative; alpha motor neurons; incidince is 1/6000 live births

Front 6

Spinal Musclular Atrophy

Back 6

autosomal recessive disease; progressive degenerative; alpha motor neurons; incidince is 1/6000 live births

Front 7

Duchenne Muscular Dystrophy

Back 7

X linked recessive; 1/3000 per male births

Front 8

Duchenne Muscular Dystrophy

Back 8

X linked recessive; 1/3000 per male births

Front 9

Bacterial vs. Eukaryotic DNA

Back 9

-Bacteria are both poly and mono cystronic
-Euk mRNA is monocistronic
-5' and 3' ends are unmodified in prok bacteria
-in euk transcription/translation occur separately

Front 10

Bacterial vs. Eukaryotic DNA

Back 10

-Bacteria are both poly and mono cystronic
-Euk mRNA is monocistronic
-5' and 3' ends are unmodified in prok bacteria
-in euk transcription/translation occur separately

Front 11

Mono cystronic

Back 11

1 mRNA coding for 1 protien

Front 12

Mono cystronic

Back 12

1 mRNA coding for 1 protien

Front 13

Polycistronic

Back 13

1 mRNA coding for more than 1 protein

Front 14

Polycistronic

Back 14

1 mRNA coding for more than 1 protein

Front 15

Dumping bacteria in new environment what hapenes?

Back 15

It turns on different metabolic pathway; it puts new genes on a single operon; and it will automatically get the same amount of required proteins

Front 16

Dumping bacteria in new environment what hapenes?

Back 16

It turns on different metabolic pathway; it puts new genes on a single operon; and it will automatically get the same amount of required proteins

Front 17

Describe EUK transcription

Back 17

messages are transcribed as premRNAs by pol2; and processed by
1. attaching a cap to the 5' end of the mRNA
2. by adding a poly A tail to the 3'end of the mRNA
3. by excising the introns to join the exons in the coding region (occurs by a large RNA protein complex called the splicosome)

Front 18

Describe EUK transcription

Back 18

messages are transcribed as premRNAs by pol2; and processed by
1. attaching a cap to the 5' end of the mRNA
2. by adding a poly A tail to the 3'end of the mRNA
3. by excising the introns to join the exons in the coding region (occurs by a large RNA protein complex called the splicosome)

Front 19

Splicing occurs in both euk and pro?

Back 19

Yes; it is the norm in EUK; PRO have way less.

Front 20

Splicing occurs in both euk and pro?

Back 20

Yes; it is the norm in EUK; PRO have way less.

Front 21

Describe Pol 2 Structure

Back 21

5' cap = 7 methyl guanosine triphosphate cap (special enzymes place this cap on/ as well as bind and recognize it)

at the end we have a signal sequence and a poly A tail

Front 22

Splicing joins excising introns

Back 22

Splicing varies in an enormous amount depending on nucleotide pairs. Sometimes the exons are incredibly small in size in comparison to the introns.

Front 23

Intronic gene

Back 23

vast majority of the DNA is used to code for introns (humans)

Front 24

what is typical of noncoding RNA

Back 24

most of them do not have any introns

Front 25

Name a few noncoding RNAs

Back 25

tRNA, miRNA, snRNA etc.

Front 26

Large variation in human genes

Back 26

average human gene is 2500 base pairs but considerable variation exists

Front 27

A typical gene contains how many introns and how many exons?

Back 27

8 and 9

Front 28

What is the gene with largest amount of exons

Back 28

Titin

Front 29

What are the 5 particles that carry out splicing?

Back 29

U1, U2, U4, U5, U6 (has to do with size)

Front 30

what about U3?

Back 30

not involved in splicing

Front 31

Describe Pol 2 Structure

Back 31

5' cap = 7 methyl guanosine triphosphate cap (special enzymes place this cap on/ as well as bind and recognize it)

at the end we have a signal sequence and a poly A tail

Front 32

Splicing joins excising introns

Back 32

Splicing varies in an enormous amount depending on nucleotide pairs. Sometimes the exons are incredibly small in size in comparison to the introns.

Front 33

Intronic gene

Back 33

vast majority of the DNA is used to code for introns (humans)

Front 34

what is typical of noncoding RNA

Back 34

most of them do not have any introns

Front 35

Name a few noncoding RNAs

Back 35

tRNA, miRNA, snRNA etc.

Front 36

Large variation in human genes

Back 36

average human gene is 2500 base pairs but considerable variation exists

Front 37

A typical gene contains how many introns and how many exons?

Back 37

8 and 9

Front 38

What is the gene with largest amount of exons

Back 38

Titin

Front 39

What are the 5 particles that carry out splicing?

Back 39

U1, U2, U4, U5, U6 (has to do with size)

Front 40

what about U3?

Back 40

not involved in splicing

Front 41

The spliceosome is made of 5 small nuclear RNA proteins called?

Back 41

snRNPs

Front 42

Systemic lupus. what happens?

Back 42

Patients develop antibodies against their own proteins including snRPS

Front 43

What is the process in which introns are excised and exons are joined together?

Back 43

Splicing

Front 44

5' end of the intron has what universal sequence?

Back 44

GU

Front 45

at 3' end of the intron has?

Back 45

AG

Front 46

The A in the intron is a ?

Back 46

branch point

Front 47

Do you know where the 5' splice site is? and the 3' splice site?

Back 47

Yes; the 2' OH of the A branchpoint attacks the 5' splice site; and you get the free floating 5' exon, which is held by the splicosome;

Front 48

What happens after the 5' exon is held on?

Back 48

the 3' OH of the 5' exon attacks the 3' splice site to join the 5' and 3' exons

Front 49

Where does this attack and ligation occur?

Back 49

on the splicesome

Front 50

Describe how spliceosome RNPs direct splicing?

Back 50

1) U1 binds to 5' splice site; branch point binding protein (BBP) and U2 auxillary factor (U2AF)
2) U2 recruitment displaces BBP and U2AF; ATP is utilized
3)U4/U5/U6 triple snRNP results in U1 snRNP dissocation; U4 dissociates and U6 base pairs with U2 that is still bound to branch point
4) ATP is used int he first step of splicing (5' OH is cut, lariate is formed)
6) ATP is indirectly used in the second step of splicing (ligation)

Front 51

U1 leaves before splicing occurs?

Back 51

Yes

Front 52

U1

Back 52

base pairs at 5' splice junction

Front 53

Helicase mediate arrangements?

Back 53

ANY TIME ATP IS USED IT's A HELICASE REACTION

5' splice site selection; helicase replaces U1 snRNP with U6 snRNP

-Branch point site selection: replace BBP and U2AF with U2 snRNP

snRNA rearrangements between 1st and 2nd step of splcing

Front 54

Helicase

Back 54

uses ATP

Front 55

Three groups of ribozymes that are involved in self catalysis?

Back 55

Group 1 No lariat
Group 2/3 Lariats

Front 56

Eukaryotic mRNAs must be capped spliced and polyadenylated?

Back 56

True

Front 57

Which pol recruits teh enzymes needed for 5' capping, splicing and 3' polyadenylation?

Back 57

Pol 2; it also transcribes the same time.

Front 58

why 5' cap first?

Back 58

5' cap is all you can do because we synthesize in 5' to 3' direction, read in 3' to 5'

to protect against the degradation, what else? because nothing else available

Front 59

Phosph only at serine 5?

Back 59

means capped

Front 60

Diphosphorylated at 2 an 5

Back 60

means it is splicing

Front 61

Singly phosphorylated at 2

Back 61

means 3' end processing

Front 62

diphosphorylation at 2 and 5

Back 62

signals splicing proteins to be recrutied

Front 63

RNA Pol2 has a CTD (c terminal domain) that is important in the recruitment of the splisozomes and phophorylations? T/F

Back 63

True

Front 64

After CTD has formed proper structure and RNA is synthesizing what happens when AAUAAA sequence is recognized?

Back 64

the CPSF and CsTF bind to the poly adenylation signal sequence and the RNA is cleaved 10-30 nucleotides downstream of the AAUAAA sequence.

Front 65

What is poly A polymerase PAP?

Back 65

Poly A Polymerase adds about 200 A groups to the 3' mRNA piece

Front 66

Does any transcription that occurs after cleavage stay on?

Back 66

No it lacks 5' cap, and poly A tail

Front 67

Poly A binding protein

Back 67

coats the poly A to prevent the chewing by nucleases

Front 68

Alternate splicing increases proteome T/F?

Back 68

True

Front 69

Intron retention?

Back 69

occurs when a particular intron is not spliced (results in different translation)

Front 70

exon skipping

Back 70

occurs if splicing skips over one or more exons (very common)

Front 71

3' / 5' splice site selection

Back 71

1st intron/ 2nd intron

Front 72

Alternate splicing makes many proteins from one gene?

Back 72

True; that's why 25000 genes code for a shit ton of proteins

Front 73

Spinal Muscular Atrophy? What is it?

Back 73

Auto Rec degenerative motor neuron disease caused by homozygous mutation of survival motor neuron gene SMN1.

Front 74

SMN1 and SMN2 are important in the?

Back 74

biogenesis of snRNPs

Front 75

Mutation in motor neruon SMN1

Back 75

causes skipping of exon 7 because it replaces an exonic splicing enhancer with an exonic splicing silencer

Front 76

ESH vs ESS

Back 76

exon 7

Front 77

Exon skipping in Duchennes Muscular Dystrophy?

Back 77

T-->A mutation leads to a stop codon. Exon skipping leads to dystrophin retaining partial activity without mutated sequence from exon 31.

Front 78

eukaryotic initiation factors

Back 78

bind to mRNA freshly exiting into the cytosol...they help circulize the mRNA