TRANSLATION

DNA TRANSLATION

Translation is the process in which ribosomes in a cell's cytoplasm create proteins, following transcription of DNA to RNA in the cell's nucleus. The entire process is a part of gene expression.

THE GENETIC CODE

THIS PROCESS INVOLVES SEVERAL KEY MOLECULES:

• mRNA Codon

• Ribosome (rRNA)

• tRNA anticodon
• 

•  The release factor

Translation proceeds in four phases:

• Amino acid activation:the amino acids (aa) are attached to their corresponding tRNA. The coupling reactions are catalysed by a group of enzymes called aminoacyl-tRNA synthetases (named after the reaction product aminoacyl-tRNA or aa-tRNA).

• Initiation: The ribosome assembles around the target mrna. The first trna is attached at the start codon.

• Elongation: The trna transfers an amino acid to the trna corresponding to the next codon. The ribosome then moves (translocates) to the next mrna codon to continue the process, creating an amino acid chain.

• Termination: When a stop codon is reached, the ribosome releases the polypeptide.

OVERVIEW OF DNA TRANSLATION

  

TRANSCRIPTION

KEY POINTS:

• Transcription is the process in which a gene's DNA sequence is copied (transcribed) to make an RNA molecule.
• RNA polymerase is the main transcription enzyme.
• Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins).
• RNA polymerase uses one of the DNA strands (the template strand) as a template to make a new, complementary RNA molecule.
• Transcription ends in a process called termination. Termination depends on sequences in the RNA, which signal that the transcript is finished.

INTRODUCTION

RNA polymerase is crucial because it carries out transcription, the process of copying DNA (deoxyribonucleic acid, the genetic material) into RNA (ribonucleic acid, a similar but more short-lived molecule).

Transcription is an essential step in using the information from genes in our DNA to make proteins. Proteins are the key molecules that give cells structure and keep them running. Blocking transcription with mushroom toxin causes liver failure and death, because no new RNA and thus, no new protein that can be made.

Transcription is essential to life, and understanding how it works is important to human health.

OVERVIEW OF TRANSCRIPTION

Transcription is the first step of gene expression. During this process, the DNA sequence of a gene is copied into RNA. Before transcription can take place, the DNA double helix must unwind near the gene that is getting transcribed. The region of opened-up DNA is called a transcription bubble.

Transcription uses one of the two exposed DNA strands as a template, this strand is called the template strand. The RNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate or coding strand. However, there is one important difference in the newly made RNA, all of the T nucleotides are replaced with U nucleotides.

The site on the DNA from which the first RNA nucleotide is transcribed is called the $+1$plus, 1 site, or the initiation site. Nucleotides that come before the initiation site are given negative numbers and said to be upstream. Nucleotides that come after the initiation site are marked with positive numbers and said to be downstream.

If the gene that's transcribed encodes a protein which many genes do, the RNA molecule will be read to make a protein in a process called translation.

Transcription initiation

To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a region called the promoter. Basically, the promoter tells the polymerase where to "sit down" on the DNA and begin transcribing.

Each gene or in bacteria, each group of genes transcribed together has its own promoter. A promoter contains DNA sequences that let RNA polymerase or its helper proteins attach to the DNA. Once the transcription bubble has formed, the polymerase can start transcribing.

ELONGATION

Once RNA polymerase is in position at the promoter, the next step of transcription elongation can begin. Basically, elongation is the stage when the RNA strand gets longer, thanks to the addition of new nucleotides. During elongation, RNA polymerase "walks" along one strand of DNA, known as the template strand, in the 3' to 5' direction. For each nucleotide in the template, RNA polymerase adds a matching (complementary) RNA nucleotide to the 3' end of the RNA strand.

The RNA transcript is nearly identical to the non-template, or coding, strand of DNA. However, RNA strands have the base uracil (U) in place of thymine (T), as well as a slightly different sugar in the nucleotide. So, as we can see in the diagram above, each T of the coding strand is replaced with a U in the RNA transcript.

The picture below shows DNA being transcribed by many RNA polymerases at the same time, each with an RNA "tail" trailing behind it. The polymerases near the start of the gene have short RNA tails, which get longer and longer as the polymerase transcribes more of the gene.

TRANSCRIPTION TERMINATION

RNA polymerase will keep transcribing until it gets signals to stop. The process of ending transcription is called termination, and it happens once the polymerase transcribes a sequence of DNA known as a terminator.

DIFFERENCES BETWEEN REPLICATION AND TRANSCRIPTION

Watch the videos for better understanding! :D

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DNA Replication

DNA REPLICATION

  

DNA Replication is the biological process by which DNA makes a copy of itself during cell division. DNA is made up of a double helix of two complementary strands. Process replication starts by separating the double helix structure of the DNA molecules. This step is known as DNA unzipping. DNA unzipping is the casual term used where the denaturation of double stranded DNA takes place. This is carried out by an enzyme called helicase which breaks the hydrogen bonds holding the complementary bases of DNA together. (A-T, C-G) . This separation forms a Y shape called replication fork and create semiconservative replication. The two separated strands then will act as templates to create new strands. 

One of the strands is known as the leading strands while the other one known as lagging strand. 

• Leading strand is oriented 5' to 3' direction toward the replication fork.
• Lagging strand is oriented 5' to 3' direction away from the replication fork.

Leading Strand

• A short pieces of RNA called primer produced by ezyme primase bind to the end of the leading strand. The primer acts as the starting point for DNA synthesis.
• DNA polymerase binds to the leading strand, adding new complementary nucleotide bases. (A,C,G,T) to the strand of DNA of the 5' 3' direction. This replication is called continuous.

Lagging Strand

• Numerous RNA primers bind at various point of along the strands.
• Chunks of DNA, called Okazaki fragments, are then added to the lagging strand also in 5' to 3' direction. 
• This sort of replication is called discontinuous.

Then, DNA polymerase synthesizes the new strands by adding nucleotides that complement each strand. DNA replication occurs during the S-stage of interphase.

There are about 5 types of DNA polymerase involved in DNA replication:

• DNA-Pol I : repair and patching of DNA.
• DNA-Pol III : responsible for the polymerization of the newly formed DNA strand.
• DNA-Pol II, IV and V : proofreading and repair enzymes.

PRIMASE 

• catalyzes the copying of a short stretch of DNA template strand to produce RNA primer sequence.

When the strands have proven that there are no mistakes in the new DNA sequences, finally, an enzyme called DNA ligase seals up the sequence of DNA into two continuous double strands. DNA replication produced two DNA molecules consisting of one new and one old chain of nucleotides (semi-conservative). Lastly, the new DNA will automatically winds up into a double helix.

Here is the video of how DNA replication occurs :

Ribonucleic acid (RNA) structures and function

RNA

• Ribonucleic acid (RNA) is a biopolymer macromolecule as DNA. It consists of small subunits called nucleotides composed of:

− Purine nucleobases [Adenine−(A), Guanine−(G)]

− Pyrimidine nucleobases [Cytosine−(C), Uracil−(U)]

− Ribose pentose sugars [C₅H₁₀O₅]

− Phosphate groups [PO₄^3-]






• The nucleobase is attached on the ribose by an glycosidic bond.
• The ribose is bonded to the phosphate group through ester bonds.

• Differences between DNA and RNA

• DNA	RNA
  A,G,C or T base	A,G,C or U base
  Double stranded	Single stranded
  2'−deoxy−D−ribose pentose sugar	D−ribose pentose sugar
  Adenine=Thymine and Guanine=Cytosine	Adenine=Uracil and Guanine =Cytosine

  
  
  
  
  
  
• RNA have 3 types which is mRNA,tRNA and rRNA.
• Messenger RNA (mRNA)-type of RNA that encodes proteins and is translated by the ribosome into proteins. Eukaryotic mRNA usually has a few different regions that look something like this:

Typical human protein coding mRNA

 Eukaryotic mRNAs undergo extensive processing directly after they are transcribed by an RNA polymerase. A cap is added on the 5′ end of the molecule which serves various functions including nuclear export, preventing exonuclease degradation, and aiding in translation initiation. A poly-A tail is also added to the 3′ end that also helps prevent mRNA degradation, among other things. Not to mention all the splicing to create the actual final mRNA.

• Transfer RNA (tRNA)-an essential component of translation, where their main function is the transfer of amino acids during protein synthesis. Therefore they are called transfer RNAs.  tRNA is the smallest of the 3 types of RNA having about 75-95 nucleotides.Each of the 20 amino acids has a specific tRNA that binds with it and transfers it to the growing polypeptide chain. tRNAs also act as adapters in the translation of the genetic sequence of mRNA into proteins. Therefore they are also called adapter molecules.Other than that,tRNAs have a clover leaf structure which is stabilized by strong hydrogen bonds between the nucleotides

• Ribosomal RNA (rRNA)-found in the ribosomes and account for 80% of the total RNA present in the cell.Though ribosomes are often described as proteins when we first learn about them, they are actually a combination of RNA and a bunch of proteins all working together.Different rRNAs present in the ribosomes include small rRNAs and large rRNAs, which denote their presence in the small and large subunits of the ribosome.

rRNAs combine with proteins in the cytoplasm to form ribosomes, which act as the site of protein synthesis and has the enzymes needed for the process. These complex structures travel along the mRNA molecule during translation and facilitate the assembly of amino acids to form a polypeptide chain. They bind to tRNAs and other molecules that are crucial for protein synthesis.

Deoxyribonucleic acid (DNA) structure

DNA

• In the mid twentieth century, geneticists were that DNA (deoxyribonucleic acid) is  genetic material.

• Functions of DNA :

1. It was able to store information for development, structure and metabolism of a cell or organism
2. It was stable so that it could be replicated with high accuracy and transmitted from generation to generation.

• DNA was located in nucleus.

• DNA based on Chargaff's Rule :DNA contains four types of nucleotides, differing in the nitrogen-containing base each contains.

1. The purine base adenine (A)
2. The pyrimidine base cytosine (C)
3. The purine base guanine (G)
4. The pyrimidine base thymine (T)

• A nucleotide from DNA contains one base, one phosphate group, and the sugar deoxyribose.

• DNA based on Franklin’s X-Ray Diffraction Studies : DNA had a helical shape

• DNA based on The Watson and Crick Model : The sugar and phosphate groups are bonded in alternating sequences to form the sides of a twisted ladder. Bases are joined by hydrogen bonds to form the rungs of the ladder.
•  Complementary base pairing occurs,meaning A only bonds with T and G with C.

There are a few level structures of Nucleic Acid.

• 1 structure : the sequence of bases along the pentose-phosphodiester backbone of a DNA                               molecule.                                                                                                                                      -base sequence of bases from the 5' end to the 3' end                                                                              - system notation single letter (A,G,C and T)

• 2 structure: the ordered arrangement of nucleid acid strands which is double helix model.

• 3 structure: three-dimensional arrangement of all atoms of nucleic acid (supercoiling)

• 4 structure: - the structure of chromatin                                                                                                      - each bead is nucleosome(DNA wrapped around histone core)