Genetics Chapter 14: RNA Molecules and RNA Processing

nucleus, cytoplasm

in eukaryotic cells, DNA resides in the ___ and proteins are made in the ___

bacteriophage infection induced RNA production

what evidence using bacteriophages found that RNA was an intermediate for protein production?

there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein

what is meant by the phrase "genes and proteins are colinear?"

no

are eukaryotic genes and proteins colinear?

the colinear protein sequence

what do codons encode?

as loops

how can noncoding regions of DNA (introns) be observed?

RNA coding regions of DNA

what are exons?

noncoding regions of DNA

what are introns?

8 to 9

how many introns does the average human gene contain?

no

are introns common in bacterial genes?

the process of removing introns from pre-mRNA and joining exons together

what is splicing?

genes of bacteria, bacteriophages, and eukaryotes

where are group I introns located?

genes of bacteria, archaea, and eukaryotic organelles

where are group II introns located?

protein-encoding genes in the nucleus of eukaryotes

where are nuclear pre-mRNA introns located?

tRNA genes of bacteria, archaea, and eukaryotes

where are transfer RNA introns located?

self-splicing

what is the splicing mechanism for Group I introns?

self-splicing

what is the splicing mechanism for Group I introns?

spliceosomal (done using a spliceosome)

what is the splicing mechanism for nuclear pre-mRNA introns?

enzymatic

what is the splicing mechanism for transfer RNA introns?

the intron itself is the enzyme that splices

what does it mean if an intron is self-splicing?

the nucleus

where does the splicing of all pre-mRNA introns take place?

it is maintained

what happens to the order of exons in DNA in spliced RNA?

protein synthesis

the mRNA is a template for ___ ___

untranslated region (UTR)

what is on the 5' end of mRNA?

a ribosome binding sequence called the Sine-Dalgarno sequence

what does the 5' untranslated region of mRNA contain?

the start codon (methionine) until the stop codon

what is the protein-coding region of mRNA?

an untranslated region (UTR) after the stop codon

what is on the 3' end of mRNA?

as it is transcribed in the nucleus

when is pre-mRNA processed in eukaryotes?

as the RNA emerges from RNA polymerase

when does 5' capping, splicing, and polyadenylation occur?

the C-terminal domain

what do enzymes associate with in RNA polymerase II?

facilitates binding of ribosome to 5' end of mRNA, increases mRNA stability, enhances RNA splicing

what is the function of the addition of a 5' cap?

increases stability of mRNA, aids in export of mRNA from the nucleus, and facilitates binding of ribosome to mRNA

what is the function of the 3' cleavage and addition of poly(A) tail?

removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing

what is the function of RNA splicing?

alters nucleotide sequence of mRNA

what is the function of RNA editing?

influence splicing, mRNA degradation, and translation

what is the function of internal RNA modifications?

coupled, regulated

in prokaryotes, transcription and translation are ___, while they are ___ in eukaryotes

the addition of an extra guanine nucleotide to the 5' end of the mRNA and the addition of methyl groups to the base in the guanine

what is the 5' cap formed by?

1. one of three phosphate groups in removed

2. guanine is added

3. methyl groups are added

what are the steps in the addition of a 5' cap?

the guanine and next two nucleotides of the trasncript

where are methyl groups added in the addition of a 5' cap?

adding about 50-250 adenine nucleotides to the 3' end of the mRNA

what is the addition of a poly(A) tail (polyadenylation)?

a sequence is recognized by the enzyme machinery, which induces a cleavage of the transcript downstream and addition of the As

how is polyadenylation initiated?

at the 5' and 3' splice junctions

where are consensus sequences for splicing located in mRNA?

branch point adenine nucleotide

what structure important for splicing is located within the intron?

the 5' splice site, the 3' splice site, and the branch point

what makes up the splicing code?

GU, AG

most introns in pre-mRNAs begin with __ and end with __

5 RNA molecules and almost 300 proteins

what does the spliceosome consist of?

an ordered sequence of two transesterification reactions

what is splicing?

RNA components that make up the spliceosome

what are snRNAs?

made up of an snRNA and multiple proteins, makes up the spliceosome

what is an snRNP?

U1, U2, U4, U5, U6

what snRNPs form the spliceosome?

1. pre-mRNA is cut at the 5' splice site

2. a cut is made at the 3' splice site and exons are joined

what are the 2 distinct steps of splicing?

the intron is released as a lariat, whose bond is broken and becomes degraded, exons are spliced together and exported to the cytoplasm to be translated

what happens when the pre-mRNA is cut at the 5' and 3' splice sites?

binds the 5' splice junction (site)

what does U1 do in splicing?

binds the branch point

what does U2 do in splicing?

form a spliceosome complex, cleaves the 5' junction and forms the branch point lariat

what do U4, U5, and U6 do in splicing?

they are dissociated

what happens to U1 and U4?

U2, U5, U6

what snRNPs are involved in the release of the lariat?

Group I and Group II

what are the two types of self-splicing introns?

introns that splice using the enzymatic activity within the intron itself

what is a self-splicing intron?

pre-mRNAs

group II introns have a similar mechanism with ___, suggesting an evolutionary relationship

pathways in which a single pre-mRNA can be processed in different ways to produce alternative types of mRNA, resulting in the production of different proteins from the same DNA sequence

what are alternative processing pathways?

alternative splicing and multiple 3' cleavage sites

what are the types of alternative processing pathways?

the same pre-mRNA can be spliced in more than one way to yield different mRNAs that are translated into different amino acid sequences and thus different proteins

what is alternative splicing?

two or more potential sites for cleavage and polyadenylation are present in the pre-mRNA

describe multiple 3' cleavage sites?

the coding sequence of an mRNA molecule is altered after transcription, so that the translated protein has an amino acid sequence that differs from that encoded by the gene

what is RNA editing?

by mechanisms that use guide RNAs, which serve as templates for RNA cleavage and nucleotide changes

how is RNA edited?

covalently

how are amino acids linked to tRNAs?

64, 20

___ codons correspond to ___ amino acids

74-95 nucleotides long and have a cloverleaf-like structure

describe the structure of tRNA

the conserved 3' CCA sequence

where are amino acids attached to tRNAs?

three nucleotides at the end of the anticodon arm which pairs with the corresponding codon on mRNA to ensure that the amino acids link in the correct order

what is the anticodon?

large (50s) and small (30s)

what are the subunits of bacterial ribosomes?

large (60s) and small (40s)

what are the subunits of eukaryotic ribosomes?

70s

what is the ribosome size of bacteria?

80s

what is the ribosome size of eukaryotes?

production of rRNA and assembly of ribosomes

what happens in the nucleolus?

help cleave and modify eukaryotic rRNAs and assemble them into mature ribosomes

what do snoRNAs do?

RNA-induced silencing complexes (RISCs)

both miRNAs and siRNAs are assembled into ___

RNA transcribed from distinct gene

what is the origin of miRNA?

mRNA, transposon, or virus

what is the origin of siRNA?

single-stranded RNA that forms short hairpins of double-stranded RNA

what does miRNA cleave?

RNA duplex or single-stranded RNA that forms long hairpins

what does siRNA cleave?

suppress gene expression by inhibiting translation

what does miRNA do?

suppress gene expression by degrading mRNA

what does siRNA do?

a powerful and precise mechanism used by eukaryotic cells to limit the invasion of foreign genes and to censor the expression of their own genes

what is RNA interference?

when there are mismatches with RISC and mRNA (miRNA)

when is translation inhibited?

when RISC and mRNA are complementary (siRNA)

when does cleavage and degradation of mRNA occur?

P element induced wimpy testis

what does Piwi stand for?

more than 200 nucleotides, some bind to proteins to prevent binding to other places acting as decoys and repressing activities, some bind to proteins and bring a set of activities together

what are long noncoding RNAs (lncRNAs)?

Xist (X-inactivation specific transcript)

what is an example of and lncRNA?

an enzyme that chops up double-stranded RNA molecules, resulting in tiny RNA molecules that are unwound to produce siRNAs and miRNAs

what is dicer?

double-stranded RNA molecules

what is RNA interference triggered by?