Lecture 15 Flashcards
(58 cards)
1
Q
colinearity
A
- concept proposed by Francis Crick
- there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein
- suggests that the number of nucleotides in a gene is proportional to the number of amino acids in the protein encoded by that gene.
2
Q
exons
A
coding regions
3
Q
introns
A
- noncoding regions
- also called intervening sequences
4
Q
After transcription
A
the introns are removed by splicing and the exons are joined to form the mature RNA
5
Q
Group I intron
A
- some rRNA genes
- self-splicing
6
Q
Group II intron
A
- protein-encoding genes in mitochondria and chloroplasts
- self-splicing
7
Q
Nuclear pre-mRNA
A
- protein-encoding genes in the nucleus
- spliceosomal splicing
8
Q
tRNA
A
- tRNA genes
- Enzymatic
9
Q
Structure of Messenger mRNA
A
INPUT IMAGE HERE!
10
Q
messenger RNA function
A
- the template for protein synthesis
- carries genetic information from DNA to a ribosome and helps to assemble amino acids in their correct order
11
Q
codon
A
a set of three nucleotides that specify for an amino acid
12
Q
5’ untranslated region
A
- leader
- Does not encode any amino acids
- contains the Shine-Delgarno sequence (in prokaryotes only)
13
Q
Shine-Delgarno sequence
A
- consensus sequence about seven nucleotides upstream of the first codon
- involved in ribosome binding during translation
- in prokaryotes only
- UAAGGAGGU
14
Q
protein-coding region
A
- comprises the codons that specify the amino acid of the protein. It begins with a start codon and ends with a stop codon.
15
Q
3’ untranslated region
A
- trailer
- not translated into protein
- affects mRNA stability and translation
16
Q
In bacteria, transcription and translation occur
A
simultaneously
17
Q
Process in bacteria
A
- while the 3’ end of an mRNA is undergoing transcription, ribosomes attach to the Shine-Delgarno sequence near the 5’ end and begin translation.
- Because the processes are coupled, there is little opportunity for modification before protein synthesis.
18
Q
transcription and translation in eukaryotes is separated
A
- temporally and spatially.
- transcription in nucleus, translation in cytoplasm
19
Q
Posttranscriptional modifications to eukaryotic pre-mRNA
A
- addition of 5’ cap
- 3’ cleavage and addition of poly(A) tail
- RNA splicing
- RNA editing
20
Q
5’ cap function
A
- facilitates binding of ribosomes to 5’ end of mRNA (initiation of translation), increases mRNA stability, enhances RNA splicing
21
Q
poly(A) tail function
A
- increases stability of mRNA,
- facilitates binding of ribosome to mRNA
22
Q
RNA splicing function
A
removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing
23
Q
RNA editing function
A
alters nucleotide sequence of mRNA
24
Q
structure of 5’ cap
A
- 7-methylguanine attached 5’ to 5’ to the mature mRNA
- methyl group added to 2’ sugar in second and third nucleotide
- initial step carried out by enzyme associated with RNA polymerase II
25
poly(A) tail
- addition of 50-250 nucleotides at the 3' end
- poly(A) nucleotides are not encoded in the DNA, but added after transcription in polyadenylation
- consensus sequence AAUAAA usually 11-30 nt upstream of cleavage site and determines where cleavage will occur
- sequence rich in uracil nucleotides typically downstream of cleavage site
- after cleavage, adenine nucleotides are added to the new 3' end, creating the poly(A) tail
26
RNA splicing
- removal of introns
- takes place in the nucleus before RNA moves to cytoplasm
- splicing requires presence of three sequences in the intron, the 5' splice site, the 3' splice site, and the branch point
- most introns begin with GU and end with CAG
27
branch point
- adenine nucleotide that lies 18-40 nucleotides upstream of 3' splice site.
- where the 5' end of the intron will bond to form a lariat
28
spliceosome
- needs three signals
- 5' consensus sequence - 9 nucleotide sequence. 3 nucleotides part of exon. 6 part of intron. This is GU at the 5' end of the intron
- 3' consensus sequence - 4 nucleotide sequence. 3 nucleotides are part of the intron. 1 part of exon. this is CAG at the 3' end of the intron
29
Steps of RNA splicing
- before splicing, intron lies between an upstream exon and a downstream exon
- pre-mRNA cut at 5' splice site. free exon 1. 5' end of intron attaches to branch point forming a lariat. G bonds to A
- cut at 3' splice site. 3' end of exon 1 attached to 5' end of exon 2. Intron released as a lariat
- intron becomes linear when the bond break at the branch point and is then rapidly degraded by nuclear enzymes.
- mature exon transported to cytoplasm where it is translated.
30
RNA splicing snRNPs
- formed by snRNA and proteins
- splicing due to interactions between mRNA and snRNAs and between snRNAs
- depend on complementary base pairing between different RNA molecules and bring components of pre-mRNA and spliceosome together
31
self splicing introns
- can remove themselves from an RNA molecule
- Group I introns
- Group II introns
32
Group I introns
- fold into a common secondary structure with nine looped stems
33
Group II introns
- also fold into secondary structures
| - intron is removed in the form of a lariat structure
34
alternative processing pathways
a single pre-mRNA can produce alternative types of mRNA resulting in the production of different proteins from the same DNA sequence
35
alternative splicing
- pre-mRNA can be spliced in more than one way.
| - yields multiple mRNAs that are translated into different amino acid sequences and thus different proteins
36
Use of multiple 3' cleavage sites
- two or more potential sites for cleavage and polyadenylation are present in the pre-mRNA
- may or may not result in a different protein depending on whether the position of the site is before or after the termination codon
37
RNA editing
- the coding sequence of an mRNA molecule is altered after transcription and thus the protein has an amino acid sequence that differs from that encoded by the gene.
- may occur through use of guide RNAs
- base pair to the pre-edited RNA and lead to addition or deletions (guide RNA serves as a template)
- adds nucleotides to the pre-mRNA that were not encoded by the DNA
38
transfer RNA
- serves as link between genetic code in mRNA and amino acids that comprise a protein
- attaches to a specific amino acid and brings it to the ribosome, where it is added to the growing polypeptide chain
- have a cloverleaf structure
39
tRNA-modifying enzymes
- allow for additional bases due to chemical modifications made to the four standard bases after transcription
40
cloverleaf structure
- structure of tRNA
- four arms of which three have a stem-loop structure
- stem formed by pairing of complementary nucleotides, and the loop lies at the terminus of the stem
41
acceptor arm
- includes the 5' and 3' of the molecule. All tRNA have the same sequence (CCA) at the end, where the amino acid attaches to the tRNA
42
anticodon arm
- at the bottom of the RNA. contains the anticodon
- made up by three nucleotides at the end of the anticodon arm
- base pairs with the corresponding codon on the mRNA during translation
43
tRNA processing
- a large precursor tRNA cleaved to produce an individual tRNA molecule
- an intron is removed by splicing and bases are added to the 3' end
- modification of several bases produces the mature tRNA
- rare bases (ribothymidine and pseudouridine)
44
ribosomes
- translate the instructions from mRNA into the amino acid sequences of proteins
- consists of small and large subunit
45
Bacterial ribosome subunit
Large 50S
| Small 30S
46
Eukaryotic ribosome subunit
Large 60S
| Small 40S
47
rRNA genes in bacteria versus eukarya
- in bacteria they are dispersed, but in eukaryotic cells they are clustered with the genes arrayed in tandem, one after another
48
two genes in eukaryotes
18S rRNA-28S rRNA-5.8S rRNA gene
| 5S rRNA gene
49
gene in prokaryotes
16S rRNA-23S rRNA-5S rRNA gene
50
small nucleolar RNAs (snoRNAs)
- help to cleave and modify the rRNAs and assemble them into mature ribosomes.
- processing of rRNA and ribosome assembly takes place in the nucleolus in eukaryotes
51
rRNA processing in prokaryotes
- methyl groups added to specific bases and to the 2' carbon atom of some ribose sugars
- The RNA cleaved into several intermediates and trimmed
- Mature rRNA molecules are the result
52
rRNA processing in eukaryotes
- methyl groups added to specific bases and to the 2' carbon atom of some ribose sugars
- the RNA cleaved into several intermediates
- Mature rRNA molecules are the result
53
three classes of small RNAs
- small interfering RNAs
- microRNAs
- piwi-interacting RNAs
54
RNA interference
- a mechanism used by eukaryotic cells to limit the invasion of foreign genes and to censor the expression of their own genes
- triggered by double-stranded RNA molecules that may arise in several ways
- speculated that evolved as a defensive mechanism against RNA viruses and transposable elements that move through RNA intermediates
55
ways double-stranded RNA might arise
- transcription of inverted repeats that then form a double stranded RNA
- simultaneous transcription of two different RNAs that are complementary to each other
- infection by viruses that make double stranded RNA
56
RNA induced silencing complex
- inverted repeats produced RNA molecule that folds into double stranded RNA
- cleaved by enzyme Dicer to produce miRNAs or siRNAs
- one strand of miRNA or siRNA combines with proteins to form a RNA induced silencing complex which pairs with mRNA and inhibits translation in case of miRNAs
- in case of siRNAs it degrades the mRNA
57
CRISPR RNA
- RNA encoded by DNA sequences in bacterial genomes termed Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)
- consists of a series of palindromic sequences, separated by unique sequences that are homologous to DNA from bacteriophage or plasmid genomes
- play a role in defense against the invasion of specific foreign DNAs such as DNA originating from bacteriophage and plasmids
58
How CRISPR works
- when bacteriophage or plasmid invades a prokaryotic cells, small portions of the invader genome are inserted as spacers between the palindromic sequences in CRISPR
- the spacer DNA serves as a memory of invader DNA. CRISPR region transcribed as single long precursor RNA which is then cleaved by CRISPR-associated proteins (Cas proteins) into crRNAs.
- these RNAs consist of a spacer sequence flanked by a part of the palindromic sequence
- when additional sequence from the same invader enters the cell, cranes pair with it and bring about cleavage of invader DNA.
