DNA and RNA Structure

DNA and RNA Structure

• DNA stands for Deoxyribonucleic acid
• DNA is arranged into a ladder-like structure called a double helix
• A DNA molecule is made of millions of tiny subunits called Nucleotides
• DNA composes of two molecules

Nucleotides

• Each nucleotide consists of a phosphate group, ribose sugar, and a nitrogenous base
• Each base will only bond with one other specific base
• Adenine (A) forms a base pair with Thymine (T)
• Cytosine (C) forms a base pair with Guanine (G)

Base-Pair Rule

• Adenine pairs with Thymine (A <==> T)
• Guanine pairs with Cytosine (G <==> C)
• The sides of the DNA ladder are phosphate and sugar held together by hydrogen bonds
• The order of the bases in one strand determines the order of the bases in the other strand due to complementary base pairing

DNA Structure and Genetic Code

• The genetic code found in DNA can be understood by looking at the sequence of bases
• The bases are arranged in triplets called codons
• A gene is a section of DNA that codes for a protein
• Each unique gene has a unique sequence of bases
• The unique sequence of bases codes for the production of a unique protein
• The proteins give us a unique phenotype
• The combination of Adenine, Thymine, Guanine, and Cytosine (A, T, G, C) determines traits
• Think of the bases of DNA like letters; letters from words and words form sentences with endless combinations.

RNA

• DNA is expressed via RNA (working copies)
• The copying process (RNA synthesis) is called transcription
• Transcription produces messenger RNA (mRNA), which is translated into amino acid sequences (translation)
• Ribonucleic acids are polyribonucleotides
• Ribonucleic acids contain mainly four nucleotides; AMP, GMP, CMP, UMP
• The nucleotides forming the structure of RNA are interconnected as in DNA by phosphodiester bonds
• RNA molecules are synthesized in a process termed transcription, and the sequence of bases in each RNA molecule is controlled by the base sequence in one strand of DNA (template strand)

DNA vs RNA

• Both are unbranched polymeric molecules
• RNA, unlike DNA, are much smaller
• RNA contains ribose (not deoxyribose)
• RNA contains uracil (not thymine)
• RNA exists mostly as single strands capable of folding into complex structures

Types of RNA

• Three main types of RNA are formed and related to protein synthesis
• Ribosomal RNA (rRNA) molecules form 80% of cellular RNA
• Transfer RNA (tRNA) forms 15% of cellular RNA.
• Messenger RNA (mRNA) molecules form 5% of cellular RNA

Ribosomal RNA (rRNA)

• rRNA are found in association with several proteins as components of the ribosomes
• Ribosomes are complex structures that serve as the site for protein synthesis by interacting with the mRNA and tRNA
• Ribosomes are made from proteins and rRNA
• Eukaryotic 80S ribosome consists of two nucleoprotein subunits of unequal size
• The 60S ribosomal subunit consists of approximately 50 polypeptides combined with three subtypes of ribosomal RNA (5S, 5.8S, 28S rRNA)
• The 40S ribosomal subunit consists of 35 polypeptides combined with one rRNA (18S rRNA)
• Both 60S and 40S combine together to form the 80 S full ribosomal subunit

Transfer RNA (tRNA)

• Transfer RNA forms about 15% of the total RNA
• The main role of tRNA is to carry and transport a specific amino acid to the ribosome during protein synthesis using an adaptor
• Recognizes the genetic code on mRNA which specifies the exact amino acid
• Each tRNA consists of 70-90 nucleotides
• tRNA consists of a single strand folded to have the shape of a cloverleaf appearance with four loops and an acceptor arm

tRNA Structure

• The acceptor arm of tRNA is at the 3' end and has the specific sequence CCA
• Amino acids are carried on the 3' end
• There are at least 20 species of tRNA molecules in every cell, at least one (and often several) corresponding to each of the 20 amino acids required for protein synthesis
• The different loops of tRNA are named according to their unique structures
• Loop I (D-loop): contains the unusual base dihydrouracil (a pyrimidine obtained by formal addition of hydrogen across the 5,6-position of uracil)
• Loop II (anticodon loop): contains three bases known as the anticodon which has anticodon sequence that can form base pairing with complementary codon of mRNA in correct position during protein synthesis
• Loop III: contains from 3-12 bases and is the major site for variation in tRNA, so termed the variable loop
• Loop IV: contains the unusual thymine and pseudouridine bases so termed the TVC loop as it contains this specific sequence

Messenger RNA (mRNA)

• Messenger RNA forms about 5% of the total RNA
• Messenger RNA is synthesized in the nucleus as a single strand with a base sequence complementary to a specific DNA region called a gene that codes the information of a certain protein
• Every three nitrogenous bases in mRNA form one codon specific for one amino acid
• If mRNA carries more than one gene it is Polycistronic, which relates to prokaryotes
• If mRNA carries information from just one gene it is Monocistronic, which relates to eukaryotes

Eukaryotic mRNA

• Eukaryotic mRNA has the following features:
• It contains coding regions (exons) that can be translated and untranslated regions in between exons called introns
• It contains noncoding segments called untranslated regions (UTRs) at both their 5' and 3' ends
• At the 5' ends there is a 7-methylguanosine triphosphate cap, and at its 3' ends there is a poly A tail, and these modified ends are created by post-transcription modification process in the eukaryotic cells
• Capping protects the 5' end of the mRNA from 5' exonuclease enzyme (catalyzes the removal of nucleotides)
• Capping helps with the transport of mRNA to the cytoplasm
• Capping helps the ribosomes to recognize of mRNA
• Capping helps the initiation of protein synthesis, where Eukaryotic mRNA lacking the cap is not efficiently translated
• The poly-A tail stabilizes the mRNA and protects it from exonucleases
• The length of the poly (A) tail determines the half-life time of mRNA
• Specifically, shortening rates act as timers for mRNA half-life, and a defined poly(A) tail length is required as an obvious starting point
• The poly-A tail increases the efficiency of translation
• The poly-A tail facilitates ribosome exit from the nucleus, and it is gradually shortened after the mRNA enters the cytosol

Gene Expression

• Gene expression in prokaryotes takes place in a single compartment
• Gene expression in eukaryotes takes place in multiple compartments in multiple stages