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DNA polymerase

DNA-directed DNA polymerase
3D structure of the DNA-binding helix-turn-helixmotifs in human DNA polymerase beta (based on PDB file 7ICG)
Identifiers
EC number | 2.7.7.7
CAS number | 9012-90-2
Databases
IntEnz | IntEnz view
BRENDA | BRENDA entry
ExPASy | NiceZyme view
KEGG | KEGG entry
MetaCyc | metabolic pathway
PRIAM | profile
PDB structures | RCSB PDB PDBe PDBsum
Gene Ontology | AmiGO / QuickGO
[show]SearchIn molecular biology, DNA polymerases are enzymes that synthesize DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential for DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones.[1][2][3][4][5][6]These enzymes catalyze the following chemical reaction deoxynucleoside triphosphate + DNAn ⇌ diphosphate + DNAn+1DNA polymerase adds nucleotides to the 3'- end of a DNA strand, one nucleotide at a time.Every time a cell divides, DNA polymerases are required to help duplicate the cell's DNA, so that a copy of the original DNA molecule can be passed to each daughter cell. In this way, genetic information is passed down from generation to generation.Before replication can take place, an enzyme called helicase unwinds the DNA molecule from its tightly woven form, in the process breaking the hydrogen bonds between the nucleotide bases. This opens up or "unzips" the double-stranded DNA to give two single strands of DNA that can be used as templates for replication.

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Before DNA can be replicated, the double stranded molecule must be “unzipped” into two single strands. DNA has four bases called adenine (A), thymine (T), cytosine (C) and guanine (G) that form pairs between the two strands. Adenine only pairs with thymine and cytosine only binds with guanine. In order to unwind DNA, these interactions between base pairs must be broken. This is performed by an enzyme known as DNA helicase. DNA helicase disrupts the hydrogen bonding between base pairs to separate the strands into a Y shape known as the replication fork. This area will be the template for replication to begin.

DNA is directional in both strands, signified by a 5' and 3' end. This notation signifies which side group is attached the DNA backbone. The 5' end has a phosphate (P) group attached, while the 3' end has a hydroxyl (OH) group attached. This directionality is important for replication as it only progresses in the 5' to 3' direction. However, the replication fork is bi-directional; one strand is oriented in the 3' to 5' direction (leading strand) while the other is oriented 5' to 3' (lagging strand). The two sides are therefore replicated with two different processes to accommodate the directional difference.

Replication Begins

Step 2: Primer Binding

The leading strand is the simplest to replicate. Once the DNA strands have been separated, a short piece of RNA called a primer binds to the 3' end of the strand. The primer always binds as the starting point for replication. Primers are generated by the enzyme DNA primase.

DNA Replication: Elongation

DNA polymerases (blue) attach themselves to the DNA and elongate the new strands by adding nucleotide bases. BSIP/UIG/Getty Images

Step 3: Elongation

Enzymes known as DNA polymerases are responsible creating the new strand by a process called elongation. There are five different known types of DNA polymerases in bacteria and human cells. In bacteria such as E. coli, polymerase III is the main replication enzyme, while polymerase I, II, IV and V are responsible for error checking and repair. DNA polymerase III binds to the strand at the site of the primer and begins adding new base pairs complementary to the strand during replication. In eukaryotic cells, polymerases alpha, delta, and epsilon are the primary polymerases involved in DNA replication. Because replication proceeds in the 5' to 3' direction on the leading strand, the newly formed strand is continuous.

The lagging strand begins replication by binding with multiple primers. Each primer is only several bases apart. DNA polymerase then adds pieces of DNA, called Okazaki fragments, to the strand between primers. This process of replication is discontinuous as the newly created fragments are disjointed.

Step 4: Termination

Once both the continuous and discontinuous strands are formed, an enzyme called exonuclease removes all RNA primers from the original strands. These primers are then replaced with appropriate bases. Another exonuclease “proofreads” the newly formed DNA to check, remove and replace any errors. Another enzyme called DNA ligase joins Okazaki fragments together forming a single unified strand. The ends of the linear DNA present a problem as DNA polymerase can only add nucleotides in the 5′ to 3′ direction. The ends of the parent strands consist of repeated DNA sequences called telomeres. Telomeres act as protective caps at the end of chromosomes to prevent nearby chromosomes from fusing. A special type of DNA polymerase enzyme called telomerase catalyzes the synthesis of telomere sequences at the ends of the DNA. Once completed, the parent strand and its complementary DNA strand coils into the familiar double helix shape. In the end, replication produces two DNA molecules, each with one strand from the parent molecule and one new strand.

Replication Enzymes

This is an illustration of a DNA polymerase molecule. DNA polymerase is an enzyme that synthesizes DNA. Callista Image/Cultura/Getty Images

DNA replication would not occur without enzymes that catalyze various steps in the process. Enzymes that participate in the eukaryotic DNA replication process include:

DNA helicase - unwinds and separates double stranded DNA as it moves along the DNA. It forms the replication fork by breaking hydrogen bonds between nucleotide pairs in DNA.

DNA primase - a type of RNA polymerase that generates RNA primers. Primers are short RNA molecules that act as templates for the starting point of DNA replication.

DNA polymerases - synthesize new DNA molecules by adding nucleotides to leading and lagging DNA strands.

Topoisomerase or DNA Gyrase - unwinds and rewinds DNA strands to prevent the DNA from becoming tangled or supercoiled.

Exonucleases - group of enzymes that remove nucleotide bases from the end of a DNA chain.

DNA ligase - joins DNA fragments together by forming phosphodiester bonds between nucleotides.

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Mutation

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Animated Video of DNA and Protein Synthesis

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DNA: G T A C C G T A T U G C U C G C C C C A U T A G A C T
mRNA: C A U G G C A U A A C G A G C G G G G U A A U C U G A
Codons: AUG GCA  AUA ACG AGC GGG GUA AUC UGA
Anti-codons: UAC CGU UAU UGC UCG CCC CAU UAG UGA
Amino acids: methionine, alanine, isoleucine, threonine, serine, glycine, valine, stop

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Protein in a cell

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Read and learn for free about the following article: Protein synthesis

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Protein Synthesis - Creative Biostructure

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Protein synthesis is process of producing proteins using information coded by DNA, located in the nucleus of a cell. Two processes are performed to convert the information in DNA into proteins by cells.

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Protein Synthesis Summary

Protein synthesis is one of the most fundamental biological processes by which individual cells build their specific proteins. Within the process are involved both DNA (deoxyribonucleic acid) and different in their function ribonucleic acids (RNA). The process is initiated in the cell's nucleus, where specific enzymes unwind the needed section of DNA, which makes the DNA in this region accessible and a RNA copy can be made. This RNA molecule then moves from the nucleus to the cell cytoplasm, where the actual the process of protein synthesis take place.

What is protein synthesis - The details!

All cells function through their proteins. Protein function is defined by their molecular function , localization within cell and involvement in a particular biological process. All components of protein function are defined by the exact composition, structure and conformation of the proteins, which is encrypted within the DNA region (called locus) encoding that protein. With the process of protein synthesis biological cells generate new proteins, which on the other hand is balanced by the loss of cellular proteins via degradation or export.

Transcription is the first of overall two protein synthesis steps. During transcription, the information encoded in the DNA is copied to a RNA molecule as one strand of the DNA double helix is used as a template. The RNA molecule is sent to the cytoplasm, which helps to bring all components required for the actual protein synthesis together - amino acids, transport RNAs, ribosomes, etc. In the cytoplasm the protein polymers are actually "synthesized" through chemical reactions - that is why the process is known as "protein synthesis" or even more precisely - "protein biosynthesis".

The RNA copy of the protein genetic information encoded in DNA molecule is produced in the nucleus and it is called messenger RNA (mRNA). Each mRNA encodes the information for a single protein and is much smaller in size compared to the DNA molecule. This makes possible for mRNA molecules to exit the nucleus through tiny openings called nuclear pores. Once it exits the nucleus and enters the cytoplasm, the mRNA could interact with a cellular structure known as a ribosome, which serves as the cell's assembler within the process of protein synthesis. The ribosome consists of proteins and ribosome RNA molecules (rRNA), which are organized in two subunits. The mRNA initially binds to just one of the ribosome sub-units.

When the mRNA interacts with the big ribosome sub-unit, this triggers the approach of another RNA molecule, called transfer RNA (tRNA). The tRNA molecule possess a specific sequence of 3-bases (anti-codon), which hast to complement a corresponding sequence (codon) within the mRNA sequence. When it finds it, it attaches to the mRNA, as the other end of the tRNA is "loaded" with an amino acid. At this point arrives the other sub-unit of the ribosome and a complete structure is formed. The first tRNA binds to a so called "start codon", which is one and the same for all proteins. As the complete ribosome structure is formed, another tRNA molecule approaches. The next tRNA differ from the first one and is carrying another amino acid. Again, the tRNA must have an anti-codon that matches complementary the second codon of the mRNA. The two amino acids carried by the first two tRNAs are bind together with help from the ribosome and using cellular energy in the form of adenosine triphosphate (ATP).

The above steps repeats until there are uncoupled codon sequences on the mRNA - thus the chain of amino acids grows longer. Once the sequence of amino acids is successfully assembled in a protein, the two ribosome sub-units separate from each other, to be joined again for later use.

The actual sequence of amino acids forms the so called primary structure of the proteins. Depending on the exact composition and order of the amino acids in the protein sequence, the chain folds into a three-dimensional shape. When this happens the protein is complete.

The process of protein synthesis takes place in multiple ribosomes simultaneous and all throughout the cell cytoplasm. A living cell can synthesize hundreds of different proteins every single second.

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What Is Protein Synthesis - Protein Synthesis

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Protein synthesis is one of the most fundamental biological processes by which individual cells build their specific proteins. Within the process are involved both DNA (deoxyribonucleic acid) and different in their function ribonucleic acids (RNA).

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What Is Protein Synthesis?

When you want to make a cake, you follow a recipe. That recipe tells you what ingredients to use and what equipment you'll need, like a mixer and bowl. When the cells of your body want to make protein, they follow a recipe.

Protein synthesis is a term that means making protein. The recipe for protein synthesis uses ingredients like mRNA, tRNA, and amino acids as well as a special piece of equipment called a ribosome. In this lesson, we'll talk about how your cells use the ingredients of protein synthesis to build new proteins inside of ribosomes.

How Does Protein Synthesis Work?

There are a lot of different proteins in your body, and each protein has its own secret code. That secret code is found inside the nucleus of your cells in a molecule called DNA. To make a new protein, the secret code has to be smuggled out of the nucleus and get into a ribosome, which is a protein-making organelle. Organelles are like tiny factories inside your cells that take care of the cells' needs.

To get the secret code from the nucleus to the ribosome, we need a messenger. The messenger that carries the genetic information from the nucleus to the ribosome is called messenger RNA, or mRNA for short.

Transcription

There are two steps of protein synthesis: transcription and translation. mRNA is made during the first step of protein synthesis, which is transcription. If you transcribe something, it means you write it down. So, in this step, the DNA's genetic information, or secret code, gets written onto a strand of mRNA. Remember that DNA is found inside the nucleus of a cell. So, transcription takes place in the nucleus.

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protein synthesis lesson for kids - video & lesson transcript | study.com

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Protein Synthesis Lesson for Kids - Video & Lesson Transcript | Study.com

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When you want to make a cake, you follow a recipe. That recipe tells you what ingredients to use and what equipment you'll need, like a mixer and bowl. When the cells of your body want to make protein, they follow a recipe. Protein synthesis is a term that means making protein.

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Inhibitors of Cell wall and protein synthesis in bacteria BDS Sem III 20-2-15

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Inhibitors of Cell wall and Protein Synthesis BDS Semester III