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Biol 2520 > Lecture 6 > Flashcards

Lecture 6 Flashcards

1
Q

Why is mRNA SPLICING required

A

It removes the introns (non coding regions)

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2
Q

Other words for introns

A

Intervening sequence

Non coding

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3
Q

What is exon and some other words

A

They the coding region of mRNA

Expressed sequence

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4
Q

What are the 2 methods of RNA splicing

A

1- Spliceosome mechanism

2- self splicing or autosplicing

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5
Q

What is a spliceosome?

A

Spliceosome is a complex protein that helps in mRNA splicing via a Spliceosome mechanism

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6
Q

What is a spliceosome made of

A

1- SnRNA( ribozymes /small nucleur RNA) + U proteins = snRNP (small nuclear ribonucleur protein / core)
2- SnRNP + other proteins + primary transcript = spliceosome

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7
Q

What does the ribozyme in spliceosome do

A

The RNA component of ribozyme (snRNA) within snRNP binds to the mRNA
The enzyme component of ribozyme within snRNP catalyses the splicing( by catalyzing the base pairing)

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8
Q

What do other proteins bound to snRNP do

A

They hold the assembly together

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9
Q

What does U proteins in spliceosome do ?

A
  • U protein Recognize each other and bind to substrate ( consensus sequence of the intron) by base pairing , using their snRNA
  • sequence identification
  • cutting of introns
  • catalyze ligation of exons together
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10
Q

Overview of mRNA splicing

A

1- SnRNPS + other proteins and primary transcript form the spliceosome
2- Splicesome cuts the intron
3- Leading to products - spliceosome components , mRNA exons bind together by ligase and cut out intron loop

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11
Q

What is a splice site

A

A splice sites are the position where spliceosome is going to cut .
These area specific sequence in pre mRNA at the beginning 5’ and end of 3’

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12
Q

What does snRNP in spliceosome do ?

A

The snRNA in snRNP binds to the splice sites
Its the snRNP molecule within spliceosome that carries out RNA SPLICING
Many snRNP ( usually labelled u1, 2, 6) carry out splicing

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13
Q

What is the enzyme and substrate in RNA splicing

A

The ribozyme (snRNA ) in the protein complex snRNP ( Us)

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14
Q

EXPLAIN in DETAIL the INTRON SPLICING

A

1- breaks ( A) are introduced at the 5’ and 3’ ends
2- sequence between exon - intron are highly conserved
3- ( exon) AG/G (intron) at 5’ and (intron) AG/G (exon)
4- these sequence are recognized by U proteins in snRNP
5- U1 snRNP Binds to the 5’ side of splice site on intron and base pairs using snRNA ( the riboenzyme catalyses the base pairing) to the pre- mRNA substrate
6- Similarly U2 snRNP binds to the branch point ( A)
7- U4/U6 and U5 bind and displace U1 - spliceosome is assemling , loop is forming
8- U4 is displaced and U6 now binds to U2
9- U5 holds the ends together while U6 carries out its job
- U6 cuts 5’ and then 3’ and joins the exon together and release the intron(lariat)

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15
Q

Function of U6

A

Cuts 5’
Cuts 4’
Joins the cut exon ends together
Release the intron

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16
Q

Function of U5

A

Holds the 2 ends together while U6 does the job

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17
Q

Basic properties of mature mRNA

A
  • each code for a specific polypeptide
  • found in the cytoplasm
  • Attach to ribosome when translated
  • only coding region translated
  • most have non coding region eg 5’UTR and 3’UTR
  • 5’ cap and 3’ tail in mature eukaryotes mRNA
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18
Q

Where is open reading frame OPR found

A

In the coding region

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19
Q

What is OPR

A

Its a continuous stretch of codons that code for the polypeptide primary structure

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20
Q

What is the function of intron

A

1- have specific DNA elements for bonding of TF
2- Reg sequence found in them, however not all of them
3- derive RNA splicing
4- Alternate splicing possible due to introns

21
Q

How is alternate splicing helpfull

A

We should know that 1 gene does not equal 1 polypeptide/ protein
1 gene can actually make many polypeptide depending on the combination of exons
For example , human cells have 22,000 genes but 100,000 different polypeptides are found
Due to alternate splicing

22
Q

What is Alternative intron splicing?

A
  • processing of identical transcript in different cells can lead to mature mRNAs with different combinations of exons thus different polypeptide/proteins formed
  • 95% of genes in humans undergo Alternate intron splicing
  • less common in other animals and rare in plants
23
Q

How do cells achieve alternative intron splicing?

A
  • exons can be skipped or included
    Skipped
  • some splice sites are weak and cannot attract the U protein to form spliceosome so thay exons can get omitted

Included/ retained
- some gnes express different splicing enhancer proteins ( these genes/ tissues are called specific expression)
Whichever exon it binds to will retain otherwise it would be removed
Eg it wont bind to mutated exons

24
Q

Examples of Alternative Splicing

A

CT / CGRP
INTRON SPLICING FOR CALCITONIN. INTRON SPLICING FOR CGRP
- forms CT mature mRNA. - forms GCRP mature mRNA
- In thyroid cells. - in neural cells
- 1, 2, 3, 4 expressed. - 1, 2, 3, 5, 6 expressed

25
Q

What is a genetic code?

A

Genetic code is a triplet codon

26
Q

How do 4 bases code for 20 amino acids - how is genetic code read

A
  • Genetic code is a triplet codom - 4to the power of 3=64 total codons
    3 are stop codon( non sense) the rest are sense codon
  • continuous , no gaps
  • no overlapping
  • code is universal shared by simplest bacteria to complex humans
  • code is degenerate
  • redundant
27
Q

What does degenrate and redundancy of geneticcode mean

A

Degenerate means that 1 AA has more then 1 codons

Redundancy means that 1 AA has more then 1 codons and therefore these multiple codon has same function

28
Q

Use / purpose of degenerate and redundancy of genetic code

A

1- when a gene (base) is mutated in the third position of a codon , it results in the same amino acid being incorporated into a protein - SILENT MUTATIONS
THEREFORE , reduces risk of mutations

29
Q

Two types of mutations while translating

A

1- synonymous (silent) mutations

2- non synonymous mutations

30
Q

Explain non synonymous mutations

A
  • mutation in the base of 1st or 2nd position of a codon , makes a different protein due to a different or no AA being incorporated
    The protein may or may not be functional
31
Q

All have same genetic code except

A

Mitochondria

Cytoplasm

32
Q

Structure of tRNA

A
  • short RNA strands of 73 to 93 nucleotides , transcribed from DNA to RNA by RNA polymerase III
  • Has internal complimentarily results in 3D structure
    • 4 short double helix with 3 loops form a 2D cloverleaf shape
    • tertiary structure gives 3D L shape
      Nucleotide
  • some modified to stabilize the tertiary structure
  • the 3 sequence nucleotides ( anticodon ) in the middle loops helps in the the recognition if the codon on mRNA
  • some nucleotides methylated after TRANSCRIPTION
  • 3’ CCA seq at the top - amino acid attachment site , helps pick the right amino acid
33
Q

Function of nucleotides in tRNA

A

Nucleotide

  • some modified to stabilize the tertiary structure
  • the 3 sequence nucleotides ( anticodon ) in the middle loops helps in the the recognition if the codon on mRNA
  • some nucleotides methylated after TRANSCRIPTION
  • 3’ CCA seq at the top - amino acid attachment site , helps pick the right amino acid
34
Q

Activation of tRNA

A
  • tRNA is activated by the addition of the right amino acid
  • this process requires energy
  • this process is catalyzed by aminoacyl - tRNA synthetases (aaRS / pirate)
  • every amino acod has a specofoc aaRS
  • recognizes all tRNAs for the specific amino acid
  • recognizes the unique part of tRNAS
  • attches the right amino acid to the CCA end
  • requires two high energy phosphate bonds - atp to amp
  • the bond formed between aa cooh ( oh ) and CCA is a high energy bond
  • the whole complex is called aminoacyl tRNA or chanrged tRNA
35
Q

Function of aaRS

A
  • recognizes all tRNAs for the specific amino acid
  • recognizes the unique part of tRNAS
  • attches the right amino acid to the CCA end
36
Q

Which reaction consumes the most energy

A

Activation of tRNA

37
Q

Imp info

A

Many of the subsequent reactions to produce a polypeptide within a ribosome are genetically favoured

38
Q

How many codons for leucine

A

Six

39
Q

How many trnas for leusine ? Why

A

4

Because 1 trna can bind to more then 1 codon

40
Q

How can 1 tRNA bind to more then 1 codom

A

Due to WOBBLE HYPOTHESIS

Due to INOSINE BASE

41
Q

What is wobble hypothesis

A

That the base pairing of the first two positions of anticodon and codon should,ld be exact however the third base isn’t supposed to match strictly

42
Q

Inosine

A

A base on anticodon that can base pair with any base

43
Q

Relationship between number of AA, codons , tRNAS

A 
There are 20 aminoacids
There are 61 codons
There are less then 61 tRNA - specifically/ majorly due to wobble hypo
Because
1 amino acid can have more then 1 codon
And 1 tRNA can bind to-more then 1 codon
44
Q

Characteristics of ribosomes

A 
Translational machinery components
Non - specific
4 rRNA and 80 small proteins
Most abundant
Free or attache to ER in cytoplasm
45
Q

Whee does rRNA transcription occurs?

A

In the nucleolus
rRNA is transcribes in the nucleolus
Ribosomes are produced in the nucleolus

46
Q

How many copies of rRNA are there

A

200 in the genome

47
Q

These copies are in 5 clusters in humans called

A

Nucleolar organizer regions

48
Q

What happens in nuclelar organizer gene

A

rRNA is transcribed
Ribosomal subunit made using ribosomal proteins
Meaning ribosomes made here
Ribosomal subunits assembled here

Then is transported to cytoplasm via nuclear pore

49
Q

rRNA transcription

A

The sequence and structure of all rRNA gene is identical
Many RNA POL I transcribe the gene forming a Christmas tree
The initial transcript is called the 45S transcript that contains 18S 5.8S and 28S rRNAs
Some are catalytic and some are structural.

Biol 2520 (16 decks)

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