bio quiz transcription and splicing

RNA

• (ribonucleic acid) is a molecule involved in using genetic information.

• Made of nucleotides

• Usually single-stranded

• Contains the bases A, U, C, G

• Found in the nucleus and cytoplasm

• Plays a key role in protein production

mRNA

• single-stranded RNA molecule that is complementary to one of the strands of DNA.

• synthesized in the nucleus (euk only)

• exits the nuclear pores to reach the cytoplasm (euk only)

• ribosome moves along the mRNA, reading the base sequence one codon at a time

• codon - triplet sequences of nitrogenous bases, each codes for a specific AA or STOP 

tRNA

• structure folds upon itself and creates an intra complementary base pairing which gives rise to hydrogen-bonded stems and loops

• The structure resembles a cloverleaf having three loops and an open end. 

• Anticodon arm of the cloverleaf recognizes and binds in a complementary fashion to the mRNA codon

• Open end with no loop is the attachment site for amino acid, via 3’ OH bonding with COOH- group of the amino acid.

• Function is to transfers the correct amino acid to growing polypeptide chain

rRNA

• single-stranded RNA molecule found ribosomes.

• function is to read and translate mRNA

• rRNA is synthesized and processed in the nucleolus, while ribosomal proteins are made in the cytoplasm. Those proteins are then imported into the nucleus for assembly with rRNA into large and small subunits, which are then exported to the cytoplasm to form functional ribosomes.

• rRNA also has enzymatic activity 

• peptidyl transferase

• catalyzes the formation of the peptide bond formed between amino acids during protein synthesis.

hnRNA (pre-mRNA)

• the unprocessed RNA transcript that is modified to become mRNA. (before splicing and modifications)

snRNA (small nuclear RNA)

• helps process mRNA by removing introns (splicing)

snoRNA (small nucleolar RNA)

• modifies and helps assemble rRNA

miRNA (microRNA)

•  regulates gene expression by reducing protein production

siRNA (small interfering RNA)

• triggers breakdown of specific mRNA molecules

lncRNA (long noncoding RNA)

• involved in gene regulation and chromatin structure

Messenger RNA (mRNA)

molecules carry information from DNA in the nucleus to the ribosome in the cytoplasm. 

Transfer RNA (tRNA)

molecules bind specific amino acids and have anticodon sequences that base pair with the codons of mRNA. tRNA is recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence. 

Ribosomal RNA (rRNA)

molecules are functional building blocks of ribosomes.

RNA Polymerase

• Enzyme that binds to a gene's promoter, unwinds the DNA double helix locally (like a zipper)

• Reads one strand to build a complementary mRNA molecule

•  —- unwinds the DNA, is creates a "transcription bubble."

• Synthesizes mRNA in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction.

Three Primary Stages in Transcription

1. Initiation - transcription factors bind to the DNA to assist in the binding of RNA polymerase to the promoter.

2. Elongation - helix unwinds, RNA polymerase adds nucleotides to the 3’ end and builds the strand 5’ to 3’

3. Termination- after the termination signal, the mRNA is released. RNA polymerase detaches.

Promoter

inding site for RNA polymerase. It is located upstream of the from the gene.

specific sequences that are recognized by RNA polymerase. Not all sequences are the same, but may have some aspects in common.

1. Nontemplate/Sense/Coding/Plus-

identical to the base sequence of the mRNA transcript (except U instead of T)

 Template/Antisense/Noncoding/Minus-

the template for making the mRNA. The mRNA sequence is complementary to the antisense strand.

termination

• when RNA polymerase encounters the termination site. 

• mRNA detaches from RNA polymerase. 

Termination sites:

Prokaryotes-

a.  may require Rho protein binding 

b. may code for inverted repeat sequences that lead to the formation of a stem-loop or hairpin structure. 

→In both cases, RNA polymerase falls off.

termination Eukaryotes-

 polyadenylation signal comprised of a sequence of U and A (AAUAAA for example) is transcribed which signals the cleavage of the mRNA and the addition of Adenine residues, creating a poly A tail. The tail contributes to stability of the mRNA.

mRNA Processing

in eukaryotic cells the mRNA transcript undergoes a series of enzyme-mediated modifications. 

i. The addition of a poly-A tail makes mRNA more stable. 

ii. The addition of a 7-methyl-guanosine cap assists with ribosomal recognition. 

iii. The excision of introns, along with the splicing and retention of exons, generates different versions of the resulting mature mRNA molecule. This process is known as alternative splicing.

in eukaryotes, there are post-transcriptional modifications.

. Add 5’cap and poly A tail: The 5’cap and poly A tail facilitate export of mRNA from the nucleus, protect it from degradation by enzymes, and help with attachment to the ribosome. Occurs in the nucleus.

2. Splice out introns and fuse exons: Introns (non-coding regions) are removed from the mRNA and the remaining exons (coding regions) are joined together to form a mature mRNA. This process is carried out by the spliceosome, a complex of small nuclear RNA (snRNA) and protein components, which catalyze the splicing reaction. Sometimes, splicing can be facilitated by a ribozyme, an RNA molecule with enzymatic activity, in self-splicing introns. Occurs in the nucleus.

spliceosome

, a complex of small nuclear RNA (snRNA) and protein components, which catalyze the splicing reaction

Capping

• involves the addition of a methyl group to the 5’-end of the transcribed RNA. (cap contains a guanine nucleotide and methyl)

• The methylated cap provides protection against degradation by exonucleases and also allows the transcript to be recognised by the cell’s translational machinery (nuclear export proteins and ribosome)

Polyadenylation

• describes the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3’-end of the transcript

• The poly-A tail improves the stability of the RNA transcript and facilitates its export from the nucleus

Splicing

• Within eukaryotic genes are non-coding sequences called introns, which must be removed (via splicing) prior to forming mature mRNA

• The coding regions are called exons and these are fused together when introns are removed to form a continuous sequence
  
  

  • In other words, introns are intruding/intervening  sequences whereas exons are expressing sequences

Alternative splicing

s a cellular process that allows a single gene to produce multiple proteins with different structures and functions. 

How? During gene expression, exons from a gene are joined in different combinations to create different messenger RNA (mRNA) transcripts. 

Result? Different mRNA transcripts are translated into proteins with different amino acid sequences and biological functions. 

Why important? It’s a major source of protein diversity in vertebrates. It's estimated that 70–88% of alternative splicing events result in changes to the encoded protein. 

Role in disease? Genomic variants in splicing regulatory sequences can disrupt splicing and cause disease. For example, the cyclin D1b variant is overexpressed in breast cancer tissues compared to normal breast tissues.