Nucleic acids
Nucleic acids:
Nucleic acids are biopolymers essential to all known forms of life. They are composed of monomers known as nucleotides. Nucleic acids are biochemical macromolecules that store and transfer genetic information in the cell. Nucleic Acids (RNA and DNA) are made up of a series of nucleotides.
Nucleotides:
A nucleotide is the basic structural unit and building block of nucleic acid. These building blocks are hooked together to form a chain of DNA.
A nucleotide is composed of 3 parts:
➢ a 5-carbon sugar
➢ a nitrogenous base
➢ a phosphate group,
Nucleosides
Nucleosides are the biochemical precursors of nucleotides.
A nucleotide is composed of 2 parts:
➢ a 5-carbon sugar
➢ a nitrogenous base Nucleoside=Sugar + Base
Nucleotide = Sugar + Base + Phosphate
Nitrogenous base: A nitrogenous base is simply a nitrogen containing molecule that has the same chemical properties as a base. They are particularly important since they make up the
building blocks of DNA and RNA. A set of five nitrogenous bases is used in the construction of nucleotides, which in turn build up the nucleic acids like DNA and RNA.
Purines and Pyrimidines are nitrogenous bases that make up the two different kinds of nucleotide bases in DNA and RNA.
The two-carbon nitrogen ring bases (adenine and guanine) are purines
The one-carbon nitrogen ring bases (thymine, Uracil and cytosine) are pyrimidines.
DNA (deoxyribonucleic acid): DNA is a type of macromolecule known as a nucleic acid. It is shaped like a twisted double helix and is composed of long strands of alternating sugars and phosphate groups, along with nitrogenous bases (adenine, thymine, guanine and cytosine).
DNA is organized into structures called chromosomes and housed within the nucleus of our cells. DNA is also found in cell mitochondria.
DNA contains the genetic information necessary for the production of cell components, organelles, and for the reproduction of life. Protein production is a vital cell process that is dependent upon DNA. Information contained within the genetic code is passed from DNA to RNA to the resulting proteins during protein synthesis.
RNA: Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids,
and, along with lipids, proteins and carbohydrates, constitute the four major macromolecules essential for all known forms of life.
Structure of DNA
The double helix of DNA has the following features:
1. It contains two polynucleotide strands around each other.
2. The backbone of each consists of alternating deoxyribose and phosphate groups.
3. The phosphate group bonded to the 5' carbon atom of one deoxyribose is covalently bonded to the 3' carbon of the next.
4. The two strands are "antiparallel"; that is, one strand runs 5′ to 3′ while the other runs 3′ to 5′.
5. The DNA strands are assembled in the 5′ to 3′ direction.
6. The purine or pyrimidine attached to each deoxyribose projects in toward the axis of the helix.
7. Each base forms hydrogen bonds with the one directly opposite it, forming base pairs.
Two-ring base (a purine) is paired with a single-ring base (a pyrimidine); A always pairs with T, and G with C as like A=T and G≡C.
8. 3.4 Å separate the planes in which adjacent base pairs are located.
9. The double helix makes a complete turn in just over 10 nucleotide pairs, so each turn takes a little more (35.7 Å to be exact) than the 34 Å shown in the diagram.
10. There is an average of 25 hydrogen bonds within each complete turn of the double helix providing a stability of binding about as strong as what a covalent bond would provide.
11. The diameter of the helix is 20 Å.
12. The helix can be virtually any length; when fully stretched, some DNA molecules are as much as 5 cm (2 inches!) long.
13. The path taken by the two backbones forms a major (wider) groove and a minor (narrower) groove.
Gene
The basic physical unit of heredity; a linear sequence of nucleotidesalong a segment of DNA that provides the coded instructions forsynthesis of RNA, which, when translated into protein , leads to the expression of hereditary character.
Genome
A genome is an organism’s complete set of DNA, including all of its genes. Each genome contains all of the information needed to build and maintain that organism. In humans, a copy of the entire genome—more than 3 billion DNA base pairs—is contained in all cells that have a nucleus.
Central dogma of biology
The central dogma of biology provides the basic framework for how genetic information flows from a DNA sequence to a protein product inside cells. This process of genetic information flowing from DNA to RNA to protein is called gene expression.
Transcription
The process of constructing a messenger RNA molecule using a DNA molecule as a template with resulting transfer of genetic information to the messenger RNA.
Transcription is the process of making an RNA copy of a gene sequence. The process by which DNA is copied to RNA is called transcription.
Translation
A step in protein biosynthesis wherein the genetic code carried by mRNA is decoded to produce the specific sequence of amino acids in a polypeptide chain. The process follows transcription in which the DNA sequence is copied (or transcribed) into an mRNA.
The process by which RNA is used to produce proteins is called translation.
Comparison between transcription and translation
Transcription Translation
Purpose The purpose of transcription is to make RNA copies of individual genes that the cell can use in the biochemistry.
The purpose of translation is to synthesize proteins, which are used for millions of cellular functions.
Definition Uses the genes as templates to produce several functional forms of RNA
Translation is the synthesis of a protein from an mRNA template. This is the second step of gene expression. Uses rRNA as assembly plant; and tRNA as the translator to produce a protein.
Products mRNA, tRNA, rRNA and non-coding RNA( like microRNA)
Proteins
Product processing
A 5’ cap is added, a 3’ poly A tail is added and introns are spliced out.
A number of post-translational modifications occur including phosphorylation, SUMOylation, disulfide bridges and farnesylation.
Location Nucleus Cytoplasm
Initiation Occurs when RNA polymerase protein binds to the promoter in DNA and forms a transcription initiation complex. Promoter directs the exact location for the initiation of transcription.
Occurs when ribosome subunits, initiation factors and t-RNA bind the mRNA near the AUG start codon.
Termination RNA transcript is released and polymerase detaches from DNA.
DNA rewinds itself into a double- helix and is unaltered throughout this process.
When the ribosome encounters one of the three stop codons it disassembles the ribosome and releases the polypeptide.
Elongation RNA polymerase elongates in the 5' - -> 3' direction
The incoming aminoacyl t-RNA binds to the codon at A-site and a peptide bond is formed between new amino acid and growing chain.
Peptide then moves one codon position to get ready for the next amino acid. It then proceeds in a 5' to 3’ direction.
Antibiotics Transcription is inhibited by rifampicin and 8-Hydroxyquinoline.
Translation is inhibited by anisomycin, cycloheximide, chloramphenicol, tetracyclin, streptomycin, erythromycin and puromycin.
Localization Found in prokaryotes' cytoplasm and in a eukaryote's nucleus
Found in prokaryotes' cytoplasm and in eukaryotes' ribosomes on endoplasmic reticulum
DNA VS RNA:
DNA (DeoxyriboNucleicAcid). RNA (Ribo NucleicAcid).
Definition A nucleic acid that contains the genetic instructions used in the development and functioning of all modern living organisms.
DNA's genes are expressed, or manifested, through the proteins that its nucleotides produce with the help of RNA.
The information found in DNA determines which traits are to be created, activated, or deactivated, while the various forms of RNA do the work.
Function The blueprint of biological guidelines that a living organism must follow to exist and remain functional. Medium of long-term, stable storage and transmission of genetic information.
Helps carry out DNA's blueprint guidelines. Transfers genetic code needed for the creation of proteins from the nucleus to the ribosome.
Structure Double-stranded. It has two nucleotide strands which consist of its phosphate group, five-carbon sugar (the stable 2- deoxyribose), and four nitrogen-containing nucleobases: adenine, thymine, cytosine, and guanine.
Single-stranded. Like DNA, RNA is composed of its phosphate group, five-carbon sugar (the less stable ribose), and 4 nitrogen-
containing nucleobases: adenine, uracil (not thymine), guanine, and cytosine.
Base Pairing Adenine links to thymine (A-T) and cytosine links to guanine (C-G).
Adenine links to uracil (A-U) and cytosine links to guanine (C-G).
Location DNA is found in the nucleus of a cell and in mitochondria.
Depending on the type of RNA, this molecule is found in a cell's nucleus, its cytoplasm, and its ribosome.
Stability Deoxyribose sugar in DNA is less reactive because of C-H bonds. Stable in alkaline conditions. DNA has smaller grooves, which makes it harder for enzymes to
"attack."
Ribose sugar is more reactive because of C-OH (hydroxyl) bonds. Not stable in alkaline conditions. RNA has larger grooves, which makes it easier to be
"attacked" by enzymes.
Propagation DNA is self-replicating. RNA is synthesized from DNA when needed.
Unique Features
The helix geometry of DNA is of B-Form.
DNA is protected in the nucleus, as it is tightly packed. DNA can be damaged by exposure to ultra-violet rays.
The helix geometry of RNA is of A- Form. RNA strands are continually made, broken down and reused. RNA is more resistant to damage by Ultra- violet rays.
Gene expression:
Gene expression refers to a complex series of processes in which the information encoded in a gene is used to produce a functional product such as a protein that dictates cell function. It involves several different steps through which DNA is converted to an RNA which in turn is converted into a protein or in some cases an RNA, for example, genes encoding the necessary information for transfer RNAs and ribosomal RNAs (tRNAs and rRNAs).
The information flow from DNA to RNA to protein can be controlled at several points helping the cell to adjust the quality and quantity of resulting proteins and thus self-regulate its functions. Thus, regulation of gene expression is a critical step in determining what kind of proteins and how much of each protein is expressed in a cell.
Fig: Steps of Gene Expression
Transcription:
Transcription is the first step in gene expression. It involves copying a gene's DNA sequence to make an RNA molecule.
• Transcription is performed by enzymes called RNA polymerases, which link nucleotides to form an RNA strand (using a DNA strand as a template).
• Transcription has three stages: initiation, elongation, and termination.
• In eukaryotes, RNA molecules must be processed after transcription: they are spliced and have a 5' cap and poly-A tail put on their ends.
Stages of transcription
Transcription of a gene takes place in three stages: initiation, elongation, and termination.
1. Initiation. RNA polymerase binds to a sequence of DNA called the promoter, found near the beginning of a gene. Each gene has its own promoter. Once bound, RNA polymerase separates the DNA strands, providing the single-stranded template needed for transcription.
2. Elongation. One strand of DNA, the template strand, acts as a template for RNA polymerase.
As it "reads" this template one base at a time, the polymerase builds an RNA molecule out of complementary nucleotides, making a chain that grows from 5' to 3'. The RNA transcript
carries the same information as the non-template (coding) strand of DNA, but it contains the base uracil (U) instead of thymine (T).
RNA polymerase synthesizes an RNA transcript complementary to the DNA template strand in the 5' to 3' direction. It moves forward along the template strand in the 3' to 5' direction, opening the DNA double helix as it goes. The synthesized RNA only remains bound to the template strand for a short while, then exits the polymerase as a dangling string, allowing the DNA to close back up and form a double helix.
In this example, the sequences of the coding strand, template strand, and RNA transcript are:
Coding strand: 5' - ATGATCTCGTAA-3' Template strand: 3'-TACTAGAGCATT-5'
RNA: 5'-AUGAUC...-3' (the dots indicate where nucleotides are still being added to the RNA strand at its 3' end)
Termination. Sequences called terminators signal that the RNA transcript is complete. Once they are transcribed, they cause the transcript to be released from the RNA polymerase. An example of a termination mechanism involving formation of a hairpin in the RNA is shown below.
The terminator DNA encodes a region of RNA that forms a hairpin structure followed by a string of U nucleotides. The hairpin structure in the transcript causes the RNA polymerase to stall. The U nucleotides that come after the hairpin form weak bonds with the A nucleotides of the DNA template, allowing the transcript to separate from the template and ending transcription. Termination of transcription, also occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.
RNA modifications:
In bacteria, RNA transcripts can act as messenger RNAs (mRNAs) right away. In eukaryotes, the transcript of a protein-coding gene is called a pre-mRNA and must go through extra processing before it can direct translation.
• Eukaryotic pre-mRNAs must have their ends modified, by addition of a 5' cap (at the beginning) and 3' poly-A tail (at the end).
• Many eukaryotic pre-mRNAs undergo splicing. In this process, parts of the pre-mRNA (called introns) are chopped out, and the remaining pieces (called exons) are stuck back together.
Types of RNA:
• mRNA - messenger RNA is a copy of a gene. It acts as a photocopy of a gene by having a sequence complementary to one strand of the DNA and identical to the other strand.
The mRNA acts as a busboy to carry the information stored in the DNA in the nucleus to the cytoplasm where the ribosomes can make it into protein.
• tRNA - transfer RNA is a small RNA that has a very specific secondary and tertiary structure such that it can bind an amino acid at one end, and mRNA at the other end. It
acts as an adaptor to carry the amino acid elements of a protein to the appropriate place as coded for by the mRNA.
• rRNA - ribosomal RNA is one of the structural components of the ribosome. Its sequence is the compliment of regions in the mRNA so that the ribosome can match with and bind to an mRNA it will make a protein from.
Translation:
Components required for translation: The key components required for translation are mRNA, ribosomes, tRNA and aminoacyl-tRNA synthetases. During translation mRNA nucleotide bases are read as three base codons, each of which codes for a particular amino acid.
The genetic code is described as degenerate because a single amino acid may be coded for by more than one codon. There are also specific codons that signal the start and the end of translation.
Each tRNA molecule possesses an anticodon on the opposite end that is complementary to the mRNA codon. tRNA molecules are therefore responsible for bringing amino acids to the ribosome in the correct order ready for polypeptide assembly.
Aminoacyl-tRNA synthetases are enzymes that link amino acids to their corresponding tRNA molecules. The resulting complex is charged and is referred to as an aminoacyl-tRNA.
Translation involves “decoding” a messenger RNA (mRNA) and using its information to build a polypeptide, or chain of amino acids.
One codon, AUG (methionine), is a “start” signal to kick off translation (it also specifies the amino acid methionine)
Translation stages
Once mRNA has left the Nucleus, it is directed to a Ribosome to construct a protein. This process can be broken down into 3 main stages:
1. Initiation:
a) Ribosome attaches to the mRNA molecule at the start codon. This sequence (always AUG) signals the start of the gene to be transcribed.
b) tRNAs (transfer RNAs) act as couriers. There are many types of tRNA, each one complimentary to the 64 possible codon combinations. Each tRNA is bonded to a specific amino acid. As AUG is the start codon, the first amino acid to be 'couriered' is always Methionine.
2. Elongation:
a) The stepwise addition of amino acids to the growing polypeptide chain. The next amino acid tRNA attaches to the adjacent mRNA codon.
b) The bond holding the tRNA and amino acid together is broken, and a peptide bond is formed between the adjacent amino acids.
c) As the Ribosome can only cover two codons at a time, it must now shuffle down to cover a new codon. This releases the first tRNA which is now free to collect another amino acid. Steps 2-5 repeats along the whole length of the mRNA molecule
3. Termination: As the polypeptide chain elongates, it peels away from the Ribosome.
During this phase, the protein starts to fold into it's specific secondary structure.
Elongation continues (perhaps for hundreds or thousands of amino acids) until the Ribosome reaches one of three possible Stop codons (UAG, UAA, UGA). At this point the mRNA dissociates from the ribosome
DNA replication:
DNA replication is the process by which DNA makes a copy of itself during cell division.
Process of DNA replication
1. The first step in DNA replication is to ‘unzip’ the double helix structure of the DNA molecule.
2. This is carried out by an enzyme called helicase which breaks the hydrogen bonds holding the complementary bases of DNA together (A with T, C with G).
3. The separation of the two single strands of DNA creates a ‘Y’ shape called a replication
‘fork’. The two separated strands will act as templates for making the new strands of DNA.
4. One of the strands is oriented in the 3’ to 5’ direction (towards the replication fork), this is the leading strand?. The other strand is oriented in the 5’ to 3’ direction (away from the replication fork), this is the lagging strand?. As a result of their different orientations, the two strands are replicated differently:
An illustration to show replication of the leading and lagging strands of DNA.
Leading Strand:
i). A short piece of RNA called a primer (produced by an enzyme called primase) comes along and binds to the end of the leading strand. The primer acts as the starting point for DNA synthesis.
ii). DNA polymerase binds to the leading strand and then ‘walks’ along it, adding new complementary nucleotide bases (A, C, G and T) to the strand of DNA in the 5’ to 3’
direction.
iii). This sort of replication is called continuous.
Lagging strand:
i). Numerous RNA primers are made by the primase enzyme and bind at various points along the lagging strand.
ii). Chunks of DNA, called Okazaki fragments, are then added to the lagging strand also in the 5’ to 3’ direction.
iii). This type of replication is called discontinuous as the Okazaki fragments will need to be joined up later.
iv). Once all of the bases are matched up (A with T, C with G), an enzyme called exonuclease strips away the primer(s). The gaps where the primer(s) were are then filled by yet more complementary nucleotides.
v). The new strand is proofread to make sure there are no mistakes in the new DNA sequence.
vi). Finally, an enzyme called DNA ligase seals up the sequence of DNA into two continuous double strands.
vii). The result of DNA replication is two DNA molecules consisting of one new and one old chain of nucleotides. This is why DNA replication is described as semi-conservative, half of the chain is part of the original DNA molecule, half is brand new.
viii). Following replication the new DNA automatically winds up into a double helix.
