RNA Synthesis (The Living Cell)

-Single stranded in eukaryotes. Double-stranded in some viruses where it carries the genetic code

-DNA to RNA to Proteins

-RNA can base pair with DNA, but not capable of forming the B form of the double helix (more A form-like)

-Because RNA single stranded – forms complicated 3D structures

B-DNA:

Most common and biologically relevant form of DNA found in living organisms.

It is a right-handed helical structure with a well-defined and regular geometry.

The B-form is the typical conformation of DNA under normal cellular conditions.

A-DNA:

A-DNA is a more compact and slightly wider helical structure compared to B-DNA.

It can be induced under certain conditions, such as dehydration or in the presence of specific ions.

Z-DNA:

Z-DNA has a left-handed helical structure,

It is characterized by a zigzag or "Z" shape.

1)Messenger RNA (mRNA)

primary transcript read from DNA

2)Transfer RNA (tRNA)

translation - carries amino acids to ribosome/mRNA complex, the anti-codon on tRNA base pairs with codon on mRNA

3)Ribosomal RNA (rRNA)

Integral to protein synthesis, providing the structural framework for ribosomes where mRNA is translated into proteins.

RNA that codes for proteins

In human cells, protein-coding mRNA typically makes up about 1-2% of the total cellular RNA.

In a cell, the majority of RNA is non-coding RNA, which includes ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), and various types of regulatory RNAs such as Small cytoplasmic (scRNA)

• Ribosomal RNA (rRNA) provides the structural framework for ribosomes where mRNA is translated into proteins

•Transfer RNA (tRNA) transports amino acids to the ribosome for protein synthesis

• Small nuclear RNA (snRNA) found in eukaryotes, is part of the splicing apparatus

• Small nucleolar RNA (snoRNA) involved in methylation of rRNA

• Small cytoplasmic RNA (scRNA) plays a role in the expression of specific genes

Maternal and Paternal

A gene is a DNA segment containing instructions for making aparticular product, including the regulatory elements.

1. Unit of heredity; contains instructions for an organism’s phenotype

2. DNA segment containing instructions for making a particular product

A gene is NOT just the bits that code for a protein

Synthesis of mRNA transcript from DNA

Protein production from mRNA transcript

1. Unwinds small portion of DNA

2. Phosphodiester bonds

3. Watson-Crick base pairs

4. Uridine-triphosphate

5. 5’→ 3’ synthesis

6. Single stranded RNA formation

DNA template

RNA polymerase II

Ribonucleotides

Buffer

Proteins required to initiate or regulate transcription in eukaryotes

Assemble on promoter to position RNA polymerase II

A. TATA box recognised by TATA-binding protein(TBP) subunit of TFIID.

B. TFIIA & TFIIB bind; TFIIA stabilises the complex.

C. Other general transcription factors(E, F, & H) bind, then RNA polymerase II assembles at the promoter, forming the transcription preinitiation complex (PIC).

D. TFIIH pulls apart the DNA helix and phosphorylates RNA Pol II.

E. Phosphorylated RNA Pol II is released from the complex and begins transcription

GC Box and the CAAT Box

+Additional upstream sequences are needed for gene-specificregulation of transcription

The primary transcript is the initial RNA molecule synthesized from a DNA template during transcription before it undergoes further processing to become a functional mRNA.

UTRs are transcribed but not translated but play essential roles in the regulation and post-transcriptional processing of mRNA

5’ UTR: regulation of translation

3’ UTR: mRNA stability & miRNA binding

1)Capping

2)Polyadenylation

3)Splicing

5' end modification:

A modified guanine nucleotide is added to the 5' end of an mRNA, forming a 5'-5' triphosphate bridge.

Guanine nucleotide:

Guanine nucleotide, is methylated at the 7th position.

Capping enzyme complex:

A capping enzyme complex, guanylyltransferase, adds the guanine cap, a methyltransferase, which methylates the guanine.

Co-transcriptional modification:

Capping is co-transcriptional

3' end modification:

A string of adenine nucleotides, (a poly(A) tail), is added to the 3' end of an mRNA molecule.

Polyadenylate polymerase:

Poly(A) polymerase adds adenine nucleotides to the mRNA transcript.

Poly(A) tail function:

Enhancing mRNA stability, facilitating nuclear export, and influencing translation efficiency.

Co-transcriptional modification:

Polyadenylation is a co-transcriptional modification.

Recognition signal:

Polyadenylation signal marks the site for poly(A) tail addition

1. Stability

2. Transport to cytoplasm

3. Integrity prior to translation

Non-coding sequences within genes

Non-coding sequences between genes

Introns and exons:

Introns are removed from the pre-mRNA, exons are joined together.

Spliceosome:

It is composed of small nuclear ribonucleoproteins (snRNPs) and other proteins.

Splice donor and acceptor sites:

Where splicing occurs, at the boundaries btt introns and exons.

Alternative splicing:

Alternative splicing allows for the generation of multiple protein isoforms from a gene by selectively including or excluding exons.

Co-transcriptional process:

It is co-transcriptional

Certain exons are excluded from the final mRNA transcript, leading to the omission (leaving out) of specific protein-coding sequences

In this case, an intron is retained in the final mRNA transcript instead of being spliced out. This intron can potentially contain stop codons, affecting the translated protein.

Different 5' splice sites within an exon are used, resulting in variations in the inclusion of specific sequences at the exon's beginning.

Different 3' splice sites within an exon are utilized, leading to variations in the inclusion of specific sequences at the exon's end.

Two or more exons are present at a particular genomic location, but only one is included in the final mRNA, leading to different protein variants.

Different promoters are used to initiate transcription, resulting in the inclusion of different first exons in the mRNA.

Various polyadenylation sites are used, leading to the inclusion of different 3' untranslated regions (UTRs) in the mRNA.