Translation / Protein synthesis.

 

• Takes place in cytoplasm.

• Messenger RNA (mRNA) brings instructions for making ONE protein from the nucleus to the ribosome.

• The mRNA binds with a small ribosomal unit.

• This binding initiates binding of a large ribosomal unit with the small ribosome unit-mRNA complex to form an assembly line for protein production.

• The large Ribosomal unit has three binding sites

• A: Attachment site.

• P: Pairing Site.

• E: Exit site.

• The completion of small ribosomal unit-mRNA- large ribosome unit complex activates movement of tRNA.

• Transfer RNA (tRNA) molecules bring amino acids from the cytosol into the ribosome to build the protein.

• Different types of tRNA bring different types of amino acids to the ribosome.

• Different types of tRNA also have different 3 base anticodon sequences that bond to mRNA “codons”. 

• The codon-anticodon binding takes place at the attachment site.

• The start codon is the first codon of a messenger RNA. It is always AUG which stands for amino acid Methionine.

• tRNA’s will only bond to mRNA where the mRNA codon complements the tRNA anticodon.

• Molecules in the ribosome covalently bond adjacent amino acids together to form the protein chain at the P site.

• The empty tRNA molecule leaves the complex at E site to bind with another amino acid.

• As the process continues, the length of amino acids grows.

• When the mRNA stop codon appears in the ribosome, the complete protein chain is released and the small ribosomal unit-mRNA- large ribosome unit complex gets separated.

Commonly Asked Questions.

1. Write a short note on “Protein Synthesis”.

2. Write a note on “translation”.

Transcription or RNA synthesis.

 

Introduction:

• Transcription is the first step in gene expression. Synthesis of an RNA molecule involves copying the DNA sequence of a gene.

• RNA polymerases, which link nucleotides to create an RNA strand using a DNA strand as a template, carry out transcription.

• Transcription has three stages: 

• initiation, 

• elongation,

• termination.

• Transcription is controlled separately for each gene in our genome.

RNA polymerase:

• RNA polymerase, the primary enzyme responsible for transcription, builds a complementary strand of RNA using a template made of single-stranded DNA. 

• Specifically, RNA polymerase builds an RNA strand in the 5' to 3' direction, adding each new nucleotide to the 3' end of the strand.

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 opens the DNA strands, providing the single-stranded template needed for transcription.

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 from complementary nucleotides, making a chain that grows in reverse, i.e. from 5' to 3'. 

• The RNA transcript uses the base uracil (U) rather than thymine (T), but it contains the same information as the non-template (coding) strand of DNA.

Termination:

• Gene 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. 

• The transcript is called “pre mRNA,” which undergoes modifications.

Modifications of pre mRNA:

• pre-mRNAs must have their ends modified, by addition of a 5' cap (at the beginning) and a 3' poly-A tail (at the end).

• Many undergo splicing. 

• In this process, non essential parts of the pre-mRNA (called introns) are chopped out, and the remaining essential parts (called exons) are joined back together.

• Modifications increase the stability of the mRNA, while splicing gives the mRNA its correct sequence.

Commonly Asked Questions.

1. Write a short note on RNA synthesis.

2. Write a short note on Transcription.

DNA Synthesis (Semiconservative Model).

 

Introduction:

• DNA replication is similar to transcription in its most general idea: a polymerase enzyme reads a strand of DNA one nucleotide at a time, it takes a random nucleotide from the nucleoplasm, and if it is complementary to the nucleotide in the DNA, the polymerase adds it to the new strand it is creating. 

• Although, there are significant differences between replication and transcription too, not the least of which is that both strands of DNA are being read simultaneously in order to create two new complementary strands that will eventually result in a complete and nearly perfect copy of an entire organismal genome.

• Models proposed for DNA Synthesis:

• Conservative Model.

• Semiconservative Model.

• Dispersive Model.

• One of the most important concepts of DNA replication is that it is a semi-conservative process. 

• It means that every double helix in the new generation of an organism consists of one complete “old” strand and one complete “new” strand wrapped around each other. 

• This is in contrast to the two other possible models of DNA replication, the conservative model, and the dispersive model. 

• A conservative mechanism of replication proposes that the old DNA is used as a template only and is not incorporated into the new double-helix. 

• Thus the new cell has one completely new double-helix and one completely old double-helix. 

• The dispersive model of replication proposes a final product in which each double helix of DNA is a mixture of fragments of old and new DNA. 

• In light of current knowledge, it is difficult to imagine a dispersive mechanism, but at the time, there were no mechanistic models at all. 

• The Meselson-Stahl experiments (1958) clearly demonstrated that the mechanism must be semi-conservative, and this was confirmed once the key enzymes were discovered and their mechanisms elucidated.

Meselson-Stahl experiments

• In these experiments, E. coli were first incubated with 15N, a heavy isotope of nitrogen. 

• Although it is only a difference in mass of one neutron per atom, there is a great enough difference in mass between heavy nitrogen-containing DNA (in the purine and pyrimidine bases) and light/normal nitrogen-containing DNA that they can be separated from one another by ultracentrifugation through a CsCl concentration gradient.

• Over 14 generations, this led to a population of E. coli that had heavy nitrogen incorporated into all of the DNA (shown in blue). 

• Then, the bacteria are grown for one or two divisions in “light” nitrogen, 14N. 

• When the DNA from the bacterial populations was examined by centrifugation, it was found that instead of light DNA and heavy DNA, as would be expected if DNA replications was conservative, there was a single band in and intermediate position on the gradient. This supports a semi-conservative model in which each strand of original DNA not only acts as a template for making new DNA, it is itself incorporated into the new double-helix.

Commonly Asked Questions.

1. Write a short note on Conservative model of DNA replication.

2. Write a short note on Meselson-Stahl experiments on DNA replication.

Structure and function of DNA and RNA.

 

Introduction:

• The organic components known as nucleic acids are found in all living things in the form of DNA or RNA. 

• These nucleic acids are created by combining nitrogenous bases, sugar molecules, and phosphate groups that are connected by various bonds in a series of sequences. 

• The fundamental genetic make-up of our body is defined by the DNA structure. 

• The Swiss biologist Johannes Friedrich Miescher first recognized and named DNA in 1869 while conducting research on white blood cells.

• James Watson and Francis Crick later made the discovery of the DNA molecule's double helix.

types of DNA.

• A-DNA: 

• The double helix is right-handed and resembles the B-DNA form.

• DNA that has been dehydrated adopts an A form that shields it from harmful conditions like desiccation. 

• Protein binding also removes the solvent from DNA, and the DNA takes an A form.

• B-DNA: 

• A right-handed helix is the most typical DNA conformation. 

• The majority of DNA has a B type conformation under normal physiological conditions.

• Z-DNA: 

• Z-DNA is a left-handed DNA whose double helix winds zigzag-style to the left. 

• Andres Wang and Alexander Rich made the discovery. 

• It is thought to play a part in gene regulation because it is located before the start site of a gene.

Structure of DNA

• DNA structure looks like a twisted ladder. 

• This structure is called a double-helix, as described in the diagram above. 

• It is a nucleic acid, and all nucleic acids are made up of nucleotides. 

• The DNA molecule is composed of units called nucleotides. 

• Nucleotides are composed of a sugar group, a phosphate group, and a nitrogen base. 

• The sugar and phosphate groups link the nucleotides together to form each strand of DNA. 

• Adenine (A), Thymine (T), Guanine (G)  and Cytosine (C) are four types of nitrogen bases.

• These four nitrogenous bases pair together in a definite way: A with T, and C with G. 

• These base pairs are essential for the DNA’s double helix structure.

• The order of the nitrogenous bases determines the genetic code or the DNA’s instructions.

• Sugar is one of the three structural elements of DNA that form the DNA molecule's backbone. 

• It is also called deoxyribose. 

• A ladder-like structure is created when the nitrogenous bases of the opposing strands form hydrogen bonds.

• The DNA molecule consists of 4 nitrogen bases, namely adenine (A), thymine (T), cytosine (C) and Guanine (G), which ultimately form the structure of a nucleotide. 

• The A and G are purines, and the C and T are pyrimidines.

• The two strands of DNA run in opposite directions. 

• These strands are held together by the hydrogen bond that is present between the two complementary bases. 

• The strands are helically twisted, where each strand forms a right-handed coil, and ten nucleotides make up a single turn.

• The pitch of each helix is 3.4 nm. Hence, the distance between two consecutive base pairs (i.e., hydrogen-bonded bases of the opposite strands) is 0.34 nm.

• The DNA coils up, forming chromosomes, and each chromosome has a single molecule of DNA in it. 

• Overall, human beings have around twenty-three pairs of chromosomes in the nucleus of cells.

Functions of DNA:

1. Carries genetic information from one generation to another.

2. Replication process.

3. Mutation – the considerable change in the sequence of DNA is called a mutation.

4. Gene therapy

5. Cellular metabolism

6. Transcription

7. DNA fingerprinting

Structure of RNA

• Ribonucleic acid (RNA) is a compound of high molecular weight essential for the synthesis of protein in cells.

• Some viruses use RNA as a genetic carrier. 

• Ribonucleotides (nitrogenous bases attached to ribose sugars) form RNA strands by attaching phosphodiester bonds. 

• With the replacement of thymine, RNA is made of the other four nitrogen bases such as adenine, cytosine, guanine, and lastly uracil, whereas in DNA instead of uracil, thymine is used. 

• RNA forms a cyclical structure that is made of one oxygen and five carbons. 

•  In 1965, R.W. Holley described the structure of the RNA molecule.

• A majority of RNA molecules are single-stranded biopolymers. 

• To fold the ribonucleotide chains into the complex structural forms that are characterized by helices and bulges, a self-complementary sequence within the RNA strand mainly plays an important role in interchain pairing. 

• RNA's three-dimensional structure is essential for its stability and function, allowing enzymes attached to the chain to attach chemical groups (e.g., methyl groups) to the ribose sugar and nitrogenous bases. 

• RNA chain contortions occur due to these modifications, which cause chemical bonds to form between distant regions of the strand. This further stabilizes the RNA structure. 

• Structures with weak stabilization and modification can easily be destroyed. 

• Also known as ribonucleoproteins (RNPs), RNAs can form complexes with these molecules. 

• It has been found that at least one RNA-containing cellular RNP acts as a biocatalyst, a function that had previously been ascribed only to proteins.

• Types of RNA:

• mRNA or Messenger RNA:

• mRNA carries genetic information from the nucleus to the cytoplasm of the cell.

• rRNA or Ribosomal RNA:

• rRNA is located in the cytoplasm of a cell, where ribosomes are found. 

• They direct the translation of mRNA into proteins.

• tRNA or Transfer RNA:

• Like rRNA, tRNA is located in the cellular cytoplasm and is involved in protein synthesis. 

• Transfer RNA brings or transfers amino acids to the ribosome that correspond to each three-nucleotide codon of rRNA.

RNA functions:

1. mRNA carries information about proteins to be synthesized by ribosomes from the nucleus.

2. rRNA directs the process of protein synthesis.

3. tRNA carries required amino acids from the cytoplasm to the ribosomes for protein synthesis.

4. tRNA also carries synthesized proteins.

Commonly asked questions.

1. Write a short note on the structure and functions of DNA and RNA.

2. Write a short note on the structure, types and functions of DNA.

3. Write a short note on the structure, types and functions of RNA.