Molecular Biology Lecture 03 - PDF

Molecular Biology Dr Nzar Shwan MLT department Lecture 03: Monday, 7th October 2024 4th Year (Semester 7) RNA Structure Let’s now turn our attention to RNA structure, which has many similarities with DNA structure....

Molecular Biology Dr Nzar Shwan MLT department Lecture 03: Monday, 7th October 2024 4th Year (Semester 7) RNA Structure Let’s now turn our attention to RNA structure, which has many similarities with DNA structure. The structure of an RNA strand is much like a DNA strand (Figure 1). Strands of RNA are typically several hundred or several thousand nucleotides in length, which is much shorter than chromosomal DNA. When RNA is made during transcription, the DNA is used as a template to make a copy of single-stranded RNA. In most cases, only one of the two DNA strands is used as a template for RNA synthesis. Therefore, only one complementary strand of RNA is usually made. Nevertheless, relatively short sequences within one RNA molecule or between two separate RNA molecules can form double-stranded regions. RNA double helices are antiparallel and right-handed, with 11 to 12 bp per turn. 1  Figure 1 A strand of RNA. This structure is very similar to a DNA strand, except that the sugar is ribose instead of deoxyribose, and uracil is substituted for thymine. In places where an RNA molecule is double-stranded, complementary regions form base pairs between A and U and between G and C. Depending on the relative locations of these complementary regions, different types of structural patterns are possible (Figure 2). These include bulge loops, internal loops, multibranched junctions, and stem-loops (also called hairpins). These structures contain regions of complementarity punctuated by regions of non-complementarity. As shown in 2  Figure 2, the complementary regions are held together by connecting hydrogen bonds, whereas the noncomplementary regions have their bases projecting away from the double-stranded region. Many factors contribute to the structure of RNA molecules, these include: 1. The hydrogen bonding between base pairs. 2. Stacking between bases. 3. The hydrogen bonding between bases and backbone regions. 4. In addition, interactions with ions, small molecules, and large proteins may influence RNA structure. Figure 2 Possible structures of RNA molecules. The double-stranded regions are depicted by connecting hydrogen bonds. Loops are noncomplementary regions that are not hydrogen bonded with complementary bases. Double-stranded RNA structures can form within a single RNA molecule or between two separate RNA molecules. Gene Structure A gene is a specific sequence of DNA containing genetic information required to make a specific protein. Types of Genes based on the organism. 1. Prokaryotic gene (which is seen in prokaryotes, for example, Bacteria, Cyanobacteria). 2. Eukaryotic gene (which is seen in higher organisms such as Plants, Animals). 3  Prokaryotic gene structure Prokaryotic Gene is composed of three regions: 1. Promoter region. 2. RNA coding sequence. 3. Terminator region.  A Prokaryotic gene is continuous, and there are no introns present.  The region 5´ of the promoter sequence is called upstream sequence and the region 3´ of the terminator sequence is called downstream sequence. 5´ 3´ Promoter region: This is situated upstream of the sequence that codes for RNA. This is the site that interacts with RNA polymerase before RNA synthesis (Transcription). Promoter region provides the location and direction to initiate transcription. Eukaryotic gene structure Eukaryotic genes are complex structures compared to prokaryotic genes. They are composed of the following regions: Exons Introns Promoter sequences Terminator sequences Upstream sequences Downstream sequences Enhancers and silencers (upstream or downstream) 4  Signals (Upstream sequence signal for addition of cap Downstream sequences signal for addition of poly A tail) Upstream (5´end) 5´UTR serve several functions including mRNA transport and initiation of translation. Signal for the addition of cap (7-methylguanosine) to the 5´end of the mRNA. The cap facilitates the initiation of translation, and stabilization of mRNA. Downstream (3´end) 3´UTR serves to add mRNA. Stability and attachment site for poly-A-tail. The translation termination codon TAA. AATAA sequence signal for addition of poly A tail. Exons Coding sequence transcribed and translated. Coding for amino acids in the polypeptide chain. Vary in number, sequence, and length. A gene starts and ends with exons (5´ to 3´). Introns Non-coding sequences, and they separate the coding sequences. They are removed when the primary transcript is processed to give the mature RNA. Introns were discovered in 1977 independently by Phillip Sharp and Richard Roberts. Promoter A promoter is a regulatory region of DNA located upstream controlling gene expression. The promoter provides a site to begin transcription. 5  Terminator Recognized by RNA polymerase as a signal to stop transcription. Promoter and terminator sequences cause RNA synthesis to occur within a defined location. Enhancer Enhances the transcription of a gene, it locates up to few thousand bp upstream. Silencers Reduce or shut down the expression of a nearby gene. Significance of Introns  Introns don't specify the synthesis of proteins but have other important cellular activities.  Many introns encode RNA’s that are major regulators of gene expression.  Contain regulatory sequences that control transcription and mRNA processing. 6  Introns allow exons to be joined in different combinations (alternative splicing), resulting in the synthesis of different proteins from the same gene.  Important role in evolution by facilitating recombination between exons of different genes (exon shuffling). INTRON SIGNIFICANCE: ALTERNATIVE SPLICING 7