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DNA Replication Steps: Replication Mechanism with Diagram
Continue ReadingDNA Replication Steps
Step 1: Replication fork formation
Step 2: Primer binding
Step 3: Synthesis of leading and lagging strands.
Step 4: Primer removal
Step 5: Proofreading, Gap filling
Step 6: End of the replication
What is DNA Replication?
In atomic science, DNA replication is the organic cycle of delivering two indistinguishable replicas of DNA from one unique DNA particle.
DNA replication happens in all living beings going about as the most fundamental part for natural legacy.
It is perused in the 3 ‘to 5’ direction by the DNA polymerase, which implies that the subsequent strand is combined in the 5 ‘to 3’ direction.
Replication includes the creation of indistinguishable DNA helices from a double stranded DNA molecule.
Catalysts are basic to DNA replication as they promote vital strides in this cycle.
The whole DNA replication measure is critical for both cell development and growth in organisms.
DNA Replication Steps
A) Initiation: Preparatory step
• Step 1: Replication fork formation.
B) Elongation: DNA Synthesis Begins
• Step 2: Primer binding
• Step 3: Synthesis of leading and lagging strands
• Step 4: Remove primer and gap fill
• Step 5: Proofreading
C) Termination:
• Step 6: End of the replication
DNA Replication Step 1: Replication Fork Formation
Before DNA can be duplicated, the double stranded molecule should be “unzipped” into two solo strands.
DNA has four bases called adenine (A), thymine (T), cytosine (C), and guanine (G) that form pair between the two strands. Adenine just combines with thymine and cytosine just ties to guanine.
To loosen up DNA, these base-pair interactions should be broken.
This is finished by a protein known as DNA helicase. Notwithstanding, there is a unique initiator protein that is needed to sets off DNA replication, to be specific DnaA.
It ties areas at the oriC site all through the cell cycle. To start the replication, notwithstanding, the DnaA protein should tie to a couple of explicit oriC groupings that have five repeats of the 9 bp arrangement also known as the R site.
At the point when DnaA ties to the oriC site, it enlists a helicase catalyst (DnaB helicase).
Presently the DNA helicase breaks the hydrogen bond that holds reciprocal DNA bases together.
The detachment of the two single strands of DNA makes a two Y-formed design called a replication fork.
Together they structure a bubble-like design called a replication bubble.
These two separate strands fill in as a layout for the creation of the new DNA strands.
Helicase is the main replication compound to be stacked at the beginning of replication. Helicase’s responsibility is to just move the replication forks forward by “unwinding” the DNA.
As we probably are aware, DNA is entirely unstable as a single strand. Along these lines, cells can keep them from returning together in a double helix.
To do this, a particular protein called single-stranded DNA binding proteins (SSBs) covers and keeps the isolated strands of DNA close to the replication fork.
When the helicase rapidly unwinds the double helix. It raises the tension on the remaining DNA particle.
Topoisomerase plays a significant support part during DNA replication. This protein forestalls the DNA double helix in front of the replication fork from turning out to be too tight when the DNA is opened.
It does this by making impermanent nicks in the helix to release tension and afterward fixing the nicks to forestall perpetual harm.
DNA Replication Step 2: Primer Binding
Another enzyme was presented in this progression, which assumes the main part in the fabrication of DNA, called as DNA polymerase.
It can just add nucleotides at the 3 ‘end of a current DNA strand. Primase forms the RNA primer, or short nucleic acid strand, that finishes the format, providing a 3 ‘end for working on DNA polymerase.
A commonplace primer has around five to ten nucleotides. The primer starts the synthesis of DNA.
When the RNA primer is set up, DNA polymerase “extends” it and consecutively adds nucleotides to make another strand of DNA that is complementary to the template strand.
DNA Replication Step 3: Synthesis of Leading and Lagging Strands
One of the strands is arranged in the 3′ to 5′ bearing (towards the replication fork), this is the leading strand.
The other strand is situated in the 5′ to 3’direction (away from the replication fork), this is the trailing strand. Due to their diverse direction.
Leading Strand Synthesis
A short piece of RNA called a primer (made by enzyme known as primase) comes by and attach to the terminal of the leading strand.
The primer fills in as the beginning stage for DNA synthesis.
The DNA polymerase ties to the leading strand and afterward strolls alongside it, adding new complementary nucleotide bases (A, C, G, and T) in the 5′ to 3′ direction to the DNA strand.
This sort of replication is known as continuous.
Lagging Strand Synthesis
The DNA polymerase consistently runs in the 5 ‘to 3’ direction.
At the point when the two strands have been incorporated consistently while the replication fork is moving.
One strand would consequently must be exposed to a 3 to 5 synthesis. Okazaki tracked down that one of the new strands of DNA was integrated in short pieces known as Okazaki fragments.
This work eventually prompted to concluded that one strand is synthesized persistently and others irregularly.
DNA polymerase III uses one bunch of its core subunits (the core polymerase) to continuously synthesize the leading strand.
While the other two sets of the core subunit lie starting with one Okazaki fragment then onto the next on the looped duct.
In vitro, there are just two arrangements of core subunits containing DNA polymerase III holoenzymes that can combine both the leading and lagging strand.
Nonetheless, the third arrangement of core subunits expands the productivity of delayed strand synthesis just as the processivity of the in general replisome.
At the point when DnaB helicase ties before DNA polymerase III.
It starts by unwinding the DNA on the replication fork as it moves alongside the trailing strand template in the 5 ‘to 3’ direction.
Primase every so often connects with DnaB helicase and synthesize a short RNA primer.
Another slide clamp is currently situated on the primer through the clamp loading complex of DNA polymerase III.
At the point when the union of the Okazaki fragment is complete. Replication stops and the core subunits of DNA polymerase III separate from their slide clamps and associate with the new clamp.
This starts the synthesis of another Okazaki fragment. Two sets of core subunits can be engaged with the union of two unique Okazaki fragments simultaneously.
When an Okazaki piece is complete, its RNA primers are taken out by DNA polymerase I or RNase H1. What’s more, that space is supplanted by DNA by the polymerase.
The leftover nick has now been fixed by the DNA ligase.
DNA Replication Step 4: Remove Primer and Gap Fill
When both the continuous and discontinuous strands are framed, an enzyme called an exonuclease (DNA polymerase I or RNase H1) eliminates all RNA primers from the first strands.
These primers were supplanted by appropriate DNA bases.
The excess nick was fixed by the DNA ligase. DNA ligase catalyzes the development of a phosphodiester bond between a 3′-hydroxyl group on the end of one strand of DNA and a 5′-phosphate on the end of another strand.
DNA Replication Step 5: Proofreading
The DNA replication happens with high constancy. It contains some unacceptable nucleotide once for each 104–105 polymerized nucleotides.
The exactness of replication relies upon the capacity of replicative DNA polymerases to choose the right nucleotide for the polymerization reaction.
This high devotion isn’t accomplished in a single step yet rather is produced through the activity of a few progressive error avoidance and processing steps.
These steps incorporate the selection of the right DNA base by the DNA polymerase, the editing of polymerase miss addition mistakes by exonucleolytic proofreading, lastly, the post-replicative DNA crisscross repair, which recognizes DNA mismatch and corrects recently replicated DNA.
Termination of DNA Replication
DNA replication stops when two forks of replication meet on a similar stretch of DNA, and the accompanying occasions happen, however not really in a specific order: forks converge until the entirety of the mediating DNA is loosened up; remaining gaps are filled and tied; Catenans are removed, and replication proteins are discharged.
DNA Replication Step 6: End of DNA Replication
At last, the parent strand and its complementary DNA strand coils into the recognizable double helix shape. The outcome is two DNA atoms comprising of one new and one old chain of nucleotides.
Every one of these two little daughter helices is an almost precise of the parental helix.
DNA Replication Steps Citations
- Origins of DNA replication. PLoS Genet . 2019 Sep 12;15(9):e1008320.
- Mechanisms of DNA replication termination. Nat Rev Mol Cell Biol . 2017 Aug;18(8):507-516.
- DNA replication origins-where do we begin? Genes Dev . 2016 Aug 1;30(15):1683-97.
- Exploiting DNA Replication Stress for Cancer Treatment. Cancer Res . 2019 Apr 15;79(8):1730-1739.
- Eukaryotic chromosome DNA replication: where, when, and how?Annu Rev Biochem . 2010;79:89-130.
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Protein Structure: Primary, Secondary, Tertiary & Quaternary
Continue ReadingWhat are Proteins?
Proteins are the building blocks from which cells are assembled.
They adopt the philosophy “structure dictates function”
Proteins are assembled from a set of 20 different a-amino acids.
They are called alpha amino acids because the amine is attached to the carbon alpha to the carbonyl group.
A protein molecule is made from a long chain of these amino acids, each linked to its neighbor through a covalent peptide bond.
Proteins, therefore, are also called polypeptides.
Each amino acid in a polypeptide chain is referred to as a residue.
There are twenty standard amino acids, each of which include a carboxyl group, a amino group, a hydrogen, and a side group all bonded to a chiral carbon center.
They typically differed only in their side chain/group, often designated as R group
Amino acids are the structural units (monomers) that make up proteins. Created with BioRender.
All amino acids residues are L-stereoisomers.
All amino acids, other than glycine, have a chiral carbon.
The position and nature of charges will depend on the pH of the solution.
Free amino acids are zwitterion at neutral pH.
The amino group is protonated and the carboxylic group is deprotonated.
Digested proteins reach the cells of the human body as single amino acids.
There are also 10 essential amino acids in humans, which means that these amino acids can’t be formed, so we must ingest them.
The amino acids are joined by peptide bonds from dehydration from the alpha- carboxyl group of one amino acid and the alpha-amino group of another.
Formed via a condensation (dehydration) reaction.
The peptide bond can exist in two conformations, cis and trans.
Peptide bonds are generally in the trans formation.
This key fact influences the types of secondary structure that form.
The sequences of peptides are always written from the N-terminal end to the C- terminal end.
Folding Patterns of Proteins
The final folded structure, or conformation, adopted by any polypeptide is determined by energetic considerations: a protein generally folds into the shape in which the free energy is minimized.
Hydrophobic, nonpolar, molecules including the nonpolar side chains of some amino acids tend to be forced together inside the folded protein thus avoiding contact with the aqueous cytosol and not disrupting hydrogen bonds that the hydrophilic, polar, amino acids are creating on the outside with H2O.
Amino acid sequence, primary structure, dictates the folding conformation of the protein and is unique to every protein.
Folding generally occurs in a step by step or hierarchical manner; local secondary structures come together to form tertiary structure etc
Types of Proteins
There are two (2) types of proteins:
1) Globular Proteins:
In which the polypeptide chain folds up into a compact shape like a ball with an irregular surface.
Enzymes are usually globular proteins.
2) Structure/Fibrous Protein:
Relatively simple, long polymers
Maintain and add strength to the cellular and matrix structure
Example: Collagen, made from a unique type of helix (triple helices of polypeptides rich in glycine and proline) and is the most abundant protein in the body.
It is very tough because it crosslinks with itself.
Most common extracellular matrix protein in the body.
Glycoproteins are proteins with a carbohydrate group attached and they are a component of cellular plasma membranes.
Also serve as markers for cellular recognition.
Proteoglycans are also a mixture of proteins and carbohydrates, buy they generally consist of more than 50% carbohydrates.
Major component of extracellular matrix.
Cytochromes are proteins which require a prosthetic (nonproteinaceous) heme group in order to function.
Cytochromes get their name from the color they add to the cell.
They are present in the METC and are responsible for electron shifting there.
Protein Structure
Primary Structure of Protein
The number and sequence of amino acids in a polypeptide is called the primary structure.
Secondary Structure of Protein
Secondary structure of proteins can be one of two (2) conformations, and result from hydrogen bonding between N-H and C=O:
a. alpha-helix:
A hydrogen bond is made between every forth peptide bond, linking the C=O of one peptide bond to the N-H of another.
Sometimes 2 a-helices will wrap around each other to form coiled-coil structure.
Occurs when the 2 a-helices have most of their nonpolar side chains on one side, so they can twist around each other.
b. beta-pleated sheets:
Made when hydrogen bonds form between segments of polypeptide lying side by side.
B-pleated sheets can be arranged into parallel B sheets and antiparallel B sheets
Parallel B sheets both neighboring polypeptides run in the same direction N-C terminus’s or C-N terminus’s
Antiparallel B sheets both neighboring polypeptides run in different directions N-C terminus’s and the other in C-N terminus’s
Secondary folding patterns aren’t uniform, they are usually broken up in the protein folding pattern with multiple alpha helices and B sheets in the protein.
The amino acid proline will disrupt both a-helix and B-pleated sheets, which assists in the creation of the tertiary structure.
Tertiary Structure of Protein
3. Tertiary structure:
The curls and folds of secondary structure to form an overall three-dimensional structure.
Most hydrophobic side chains are buried away from water
Typically compact
Most charged chains are on the outer face hydrated to water molecules
The biggest contributing factor to tertiary structure come from the hydrophobic forces
Tertiary structures are stabilized by Hydrogen bonding, Electrostatic interactions, van der Waals forces, hydrophobic forces, covalent disulfide bonds, between two cysteine amino acids on different parts of the chain.
Quaternary Structure of Protein
4. Quaternary structure:
When two or more polypeptide chains bind together.
The same 5 forces at work in tertiary structure can also act to form the quaternary structure.
Protein Stablization
When a cell is exposed to extracellular conditions they will create covalent cross- linkages , both intra and inter.
Most often they are disulfide bonds, and they do not change the conformation of the protein, but instead reinforce it.
Disulfide bonds occur between 2 cysteine amino acids.
Disulfide bonds usually don’t form in the cell cytosol, because of a high concentration of reducing agents
A protein can be unfolded, or denatured, by treatment with certain solvents that disrupt the noncovalent interactions holding the folded chain together.
When a protein is denatured all that remain is the primary structure.
When the denaturing solvent is removed the protein often refolds spontaneously, or renatures, into its original conformation, this indicates that the primary structure is what determines the folding pattern of the protein.
Many proteins require helper proteins called molecular chaperones to help fold into the proper energetically favorable tertiary native structure.
Protein Destabilizing Agents
Denaturing Agents Forces Disrupted Urea Hydrogen bonds Salt or pH change Electrostatic forces Mercaptoethanol Disulfide bonds Organic solvents Hydrophobic forces Heat All forces Protein Citations:
- A mathematical framework for protein structure comparison
- Protein structure prediction based on sequence similarity
- A structure-centric view of protein evolution, design, and adaptation
- Classification of Protein Structure Classes on Flexible Neutral Tree
- Bridging protein structure, dynamics, and function using hydrogen/deuterium-exchange mass spectrometry
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Lipids: Structure, Types, Examples, Functions, Types
Continue ReadingLipids Definition
A lipid is any biological molecule that has low solubility in water and high solubility in nonpolar organic solvents.
Types of Lipids and Lipids Function
There are six major groups of lipids:
1. Fatty Acids
a. Building blocks for most, but not all, complex lipids
b. Usually an even number of carbons, maximum # of carbons in humans is 24
c. Oxidation of fatty acids liberates large amounts of chemical energy for the cell, and most lipids reach the cell in the form of fatty acids and NOT as triacylglycerols.
d. Can be saturated or unsaturated
Saturated Fatty Acids contain only single carbon-carbon bonds
Unsaturated fatty acids contain one or more carbon-carbon double bonds
Saturated Fatty Acid
Unsaturated Fatty Acid
2. Triacylglycerols
a. Commonly called triglycerides or simply fats and oils, are constructed from a three carbon backbone called glycerol, which is attached to 3 fatty acids
b. Their function is to store energy and may also provide thermal insulation and padding to an organism
Example and structure of an unsaturated fat triglyceride
Fat in adipose tissue
c. Adipocytes, also called fat cells, are specialized cells whose cytoplasm contains almost nothing but triglycerides.
d. Lypolysis of triacylglycerols take place inside the adipose cells when blood levels of epinephrine, norepinephrine, glucagon or ACTH are high!!
3. Phospholipids
a. Are built from a glycerol backbone as well, but a polar phosphate group replaces one of the fatty acids.
b. The phosphate group lies on the opposite side of the glycerol from the fatty acids making this lipid polar on one end and nonpolar on the other end.
Phospholipids
Phospholipid arrangement in cell membranes.
c. This condition is called amphipathic, and makes phospholipids especially well suited as the major component of membranes
4. Glycolipids
a. Are similar to phospholipids, except that glycolipids have one or more carbohydrates attached to the 3-carbon glycerol backbone instead of the phosphate group.
b. Are also amphipathic
Structural arrangment of glycolipids
c. They are found in abundance in the membranes of myelinated cells composing the nervous system.
d. Also serve as markers for cellular recognition.
5. Steroids
a. are four ringed structures, which regulate metabolic activities.
b. Include some hormones, vitamin D, and cholesterol, an important membrane component.
6. Terpenes
a. include vitamin A, a vitamin important for vision
b. Their building block is the hydrocarbon isoprene, CH2=C(CH3)-CH=CH2 . Terpene hydrocarbons therefore have molecular formulas (C5H8)n
7. 20 Carbon Eicosanoids
a. Eicoanoids include prostaglandins, thromboxanes, and leukotrienes
b. Eicosanoids are released from cell membranes as local hormones that regulate, among other things, blood pressure, body temperature, and smooth muscle contraction.
c. Aspirin is a commonly used inhibitor in prostaglandin synthesis
d. Since lipids are insoluble in aqueous solution, they are transported in the blood via lipoproteins.
e. A lipoprotein is a biochemical assembly that contains both proteins and lipids.
f. It contains a lipid core surrounded by phospholipids and apoproteins.
g. Thus lipoproteins are able to dissolve lipids in its hydrophobic core, and then move freely through the aqueous solution due to its hydrophilic shell
h. Lipoproteins classified according to density.
The greater the ratio of lipid to protein, the lower the density.
i. The major classes of lipoproteins are chylomicrons, very low density lipoproteins (VLDL), low density lipoproteins (LDL – “bad cholesterol”), and high density lipoproteins (HDL – “good cholesterol”) – is arranged according to density.
Lipids Citations:
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