Category: Biology
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Lactobacillus: Health Benefits, Uses, and Side Effects
Continue ReadingAbout Lactobacillus
Microorganisms comprises of varied microbes, fungi, protozoa. It also includes many microscopic plants viruses, viroid and also prions.
They can be seen anywhere on this planet anywhere where habitat is seen. It can flourish on nutritive media where researchers can do studies on it by cultivation and producing colonies and can help for research purpose.
Microorganisms gives rise to various diseases in living beings including plants and animals, although they cause diseases, they can be useful in many different and friendly ways.
One such type of bacteria is lactobacillus and there are many species of lactobacillus which are useful and can help in digestion, and on urinary and reproductive system as well and cause no harm.
They are also used in various consumable forms such as yogurts and probiotic drink or supplements.
It is most popular to treat diarrhea when patients are given antibiotics which may suppress the gut flora and this type of bacteria helps to protect and increase good gut flora which prevents it.
Lactobacillus contributes significantly in improving the overall health in living beings.
They are also used and prescribed for general digestion problems, large intestine disorders which causes stomach pain, irritable bowel syndrome (IBS), colic in infants, inflammation of bowel track or colon, etc.
It is a gram-positive, aerotolerant anaerobes or microaerophilic, rod-shaped, non-spore-forming bacteria under the genus Lactobacillus and has as many as 260 phylogenetically, metabolically varied species.
Its taxonomic update of the genus in 2020 put lactobacilli to 25 genera.
Metabolism of Lactobacillus
They are the only group of the lactic acid bacteria that comprises of homofermentative and heterofermentative organisms and in the Lactobacillaceae, either metabolism is jointly used by all strains of Lactobacillus.
In Lactobacilli hexoses are metabolised by glycolysis to lactate as higher end product which is termed as homofermentative.
It may be heterofermentative, which means that hexoses are broken down by the Phosphoketolase pathway to lactate, CO2 and acetate or ethanol as the end product.
They are aerotolerant which means it is manganese-dependent and has been seen in Lactiplantibacillus plantarum.
Few lactobacillus species respire only if heme and menaquinone are available in the growth medium but usually don’t need iron for development.
This species is homofermentative, do not exhibit pyruvate formate lyase, and manty don’t ferment pentoses example: in L. crispatus, pentose metabolism is strain selective and is gained by lateral gene transmit.
Genome of Lactobacillus
The genome is not constant and differs, size from 1.2 to 4.9 Mb (megabases) and the quantity of protein-coding genes vary from 1,267 to about 4,758 genes in Fructilactobacillus sanfranciscensis and Lentilactobacillus parakefiri.
Differences can be seen in one species as well for example in L. crispatus genome sizes varies in between 1.83 to 2.7 Mb, or 1,839 to 2,688.
Lactobacillus comprises a stock of compound microsatellites in the coding area that are not perfect and usually possess different motifs and they also comprises of many plasmids.
In many new research study they have delineated that the plasmids encode the genes which are necessary to acquittance of lactobacilli to the surrounding.
Types of Lactobacillus
L. delbrueckii is a type of species of the genus, is 0.5 to 0.8 μm and can be seen in single or in small groups in chains.
L. acidophilus, L. brevis, L. casei, and L. sanfranciscensis are some another types.
The quantity of lactic acid generated differs. In L. brevis and L. fermentum, glucose metabolism is heterofermentative, with lactic acid sums upto 50% of end products and ethanol, acetic acid, and carbon dioxide as the rest 50%.
The organisms that cannot metabolise glucose receives its energy organic components like galactose, malate, or fructose.
Health Benefits of Lactobacillus
Lactobacillus spp. are fundamental as purposeful and essential as deliberate or accidental component in many food available.
An excellent deal of attention has been given to its significant property as being probiotics.
Strains that are evaluated for this beneficial property comprises of L. acidophilus LA1, L. acidophilus NCFB 1748, Lactobacillus GG, L. casei Shirota, Lactobacillus gasseri ADH, and Lactobacillus reuteri.
Other beneficial property of Lactobacillus accommodates immune improvements, decreasing fecal enzyme process, inhibiting intestinal disorders, and decreasing incidence of viral diarrhea and this probiotic strains are said to own a capability to live in/habitat in the intestinal tract, and in a good way affecting the microflora and maybe excluding colonization by pathogens.
Albeit the positive effects from having of probiotics is critical, authentic records still remains in water and the clinical trials often have hurdles and costly to conduct specially in people within which compliance with experimental protocols and normalizing for other genetic and environmental factors are hard.
For now the major focus is onselective isolates, such as L. casei GG, and research is directed and is being built around these strains.
Ergo, variety of products are named as probiotics and are clubbed together with more traditional dairy products to be sold in the market. This are easily available for the normal people.
Lactobacillus spp. are important components in many food products which either we know or may be present unknowingly.
Significant amount of attention has been directed toward their potential benefits and importance as probiotics.
Strains that have been verified for their probiotic properties are L. acidophilus LA1, L. acidophilus NCFB 1748, Lactobacillus GG, Lactobacillus casei, L. Shirota, gasseri ADH, and Lactobacillus reuteri.
Many reported clinical effects attributed to the consumption of it consist of immune enhancement, lowering faecal enzyme activity, preventing intestinal problems, and reducing viral diarrhoea.
Most probiotic strains are accepted to have a capacity to colonize the intestinal lot, subsequently decidedly influencing the microflora and maybe barring colonization by microbes.
But the possible advantages from the utilization of probiotics are huge, research is as yet slacking.
Clinical preliminaries are troublesome and costly to perform particularly in people in which consistency with trial conventions and normalizing for other hereditary and natural components are troublesome.
Huge worth and spotlight are currently being set on specific confines, like L. casei GG, and protected innovation is being worked around these strains.
These are filled in milk and split it to frame curd. The LAB creates acids that coagulate and do not completely digest the milk proteins which upgrades the wholesome property by raising vit. B12.
Presently, various items are assigned as probiotics and are sold alongside more conventional dairy items.
Probiotics especially related to Bifidobacterium spp. and Lactobacillus spp. have studied and research shows that they exhibit anticarcinogenic, antimutagenic, and antitumorigenic activities ergo, more research needs to be executed to verify its authenticity.
Lactobacillus Citations
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Proto-Oncogene: Definition, Function, and Examples
Continue ReadingWhat are Proto-Oncogene?
There are trillions of living cells in the body that develops, gap and bite the dust in a systematic design. This cycle is firmly directed by the qualities inside a cell’s core.
These qualities code for proteins that assist with controlling cell development. These significant qualities are called proto-oncogenes.
An adjustment of the DNA grouping of the proto-oncogene brings about an oncogene, which delivers an alternate protein and meddles with typical cell guidelines.
Features of Proto-Oncogene
Protooncogenes have numerous capacities in a cell however they regularly code for proteins that animate cell division, forestall cell separation, or manage customized cell demise (apoptosis).
These are for the most part fundamental cycles needed for ordinary development, improvement, and the support of solid organs and tissues.
Notwithstanding, a changed or blemished adaptation of a proto (oncogene) expands the creation of these proteins, subsequently prompting unregulated cell division, a slower pace of cell separation, and expanded hindrance of cell demise.
Combined this enhances and highlights properties of the cells that have gotten malignant.
Presently, scientists know about in excess of 40 unique sorts of proto-oncogenes in people.
A few hereditary components that cause a proto-oncogene to turn into an oncogene have additionally been clarified and models are given underneath:
• Point transformations, inclusions or erasures that lead to an overactive quality item.
• Point transformations, inclusions or cancellations that lead to an expansion in record.
• Quality intensification prompting extra duplicates of a proto-oncogene.
• Chromosomal movement that makes a proto-oncogene move to an alternate chromosomal site related with expanded articulation.
• Chromosomal movements that cause a protooncogene to intertwine with another quality to deliver a protein that has oncogenic action.
Proto-Oncogene Characteristic
A couple of malignancy conditions are brought about by acquired changes of proto-oncogenes that cause the oncogene to be turned on (initiated).
However, most disease-causing changes including oncogenes are obtained, not acquired.
They, by and large, actuate oncogenes by:
Chromosome modifications: Changes in chromosomes that put one quality close to another, which permits one quality to initiate the other.
Quality duplication: Having additional duplicates of a quality, which can prompt it making an over-the-top certain protein.
Investigation into oncogenes has worked on comprehension and information regarding why certain people are more helpless to malignant growth than others.
A few bunches are bound to have their proto-oncogenes changed over to oncogenes and foster malignancy.
The specialists that cause malignant growth like radiation, infections, and ecological poisons, for instance, are bound to cause disease in these people.
Example of Proto-Oncogene: HER2
One illustration of a notable proto-oncogene is the HER2 quality. This quality codes for a transmembrane tyrosine kinase receptor called human epidermal development factor receptor 2.
HER2 Receptor and Breast Cancer
This protein receptor is associated with the development, fix, and division of cells in the bosom.
In a sound breast cell, there are two duplicates of HER2, yet in certain kinds of bosom malignant growth, the cells contain multiple duplicates, which prompts overabundance creation of the HER2 protein.
This makes the breast cells develop, partition and multiply considerably more rapidly than sound breast cells.
HER2/EGFR signaling pathway in Breast cancer
This hereditary deformity in the Breast cells isn’t acquired yet is well on the way to emerge because of maturing.
Specialists are as yet exploring whether natural factors, for example, smoke and contamination improve the probability of the imperfection happening.
In the event that a lady is analyzed as HER2 positive, she has a strange number of HER2 qualities and is creating a lot of the HER2 protein.
This implies cells in her Breast are filling in an upregulated way and shaping a carcinogenic tumor.
Assuming a lady is analyzed as HER2 negative, it’s anything but HER2 protein creation that is causing malignant growth.
Example of Proto-Oncogene: Myc
Another illustration of a proto-oncogene is the Myc quality, which codes for record factors.
At the point when the quality grouping of Myc is modified, these record factors are created at expanded rates and quality articulation is changed bringing about the arrangement of a tumor.
What is Oncogene?
On the contrary oncogenes are qualities that leads to malignancies.
As such, oncogenes can be characterized as destructive qualities. Oncogenes are transformed proto-oncogenes. At the point when the DNA succession of the proto-oncogene is changed or transformed, it’s anything but an oncogene.
Oncogene is coded with various proteins which impact the ordinary cell cycle.
Oncogenes produce inhibitors of the phone cycle which are equipped for proceeding with cell division in any event, during conditions that are not useful for cell division.
Oncogenes additionally produce positive controllers which are fit for keeping cells dynamic till the development of malignant growth.
Oncogenes run after disease development by advancing uncontrolled cell division, bringing down cell separation and restraining ordinary cell demise (apoptosis).
Proto-oncogenes become oncogenes because of a few hereditary changes or systems like transformations, quality intensifications, chromosomal movements.
They are rattled off as follows.
Creation of overactive quality items by point transformations, inclusions, or erasures.
Expanded record by point transformations, inclusions or erasures.
Creation of extra duplicates of proto-oncogenes by quality intensification.
Development of proto-oncogenes into various chromosomal site and cause for expanded articulation.
Combination of proto-oncogenes with different qualities which can cause oncogenic action.
Examples
HER2: Another notable protooncogene is HER2. This quality makes protein receptors that are engaged with the development and division of cells in the breast.
Numerous individuals with breast disease have a quality intensification transformation in their HER2 quality.
This kind of disease is frequently alluded to as HER2-positive breast malignant growth.
Myc : The Myc quality is related with a sort of malignant growth called Burkitt’s lymphoma.
It’s anything but a chromosomal movement moves a quality enhancer arrangement close to the Myc proto-oncogene.
Cyclin D: Cyclin D is another protooncogene. Its ordinary occupation is to make a protein called Rb tumor silencer protein dormant.
In certain diseases, similar to tumors of the parathyroid organ, Cyclin D is actuated because of a change.
Thus, it can presently don’t manage its work of making the tumor silencer protein inert.
This thus causes uncontrolled cell development.
Your cells contain numerous significant qualities that direct cell development and division.
The typical types of these qualities are called proto-oncogenes. The changed structures are called oncogenes. Oncogenes can prompt disease.
You can’t totally keep a change from occurring in a proto-oncogene, yet your way of life may have an effect.
You might have the option to bring down your danger of malignancy causing changes by opting for heathier lifestyle.
Citations
- Proto-oncogene fos: complex but versatile regulation. Cell . 1987 Nov 20;51(4):513-4.
- Proto-oncogene fos: an inducible gene. Princess Takamatsu Symp . 1986;17:279-90.
- A function for the lck proto-oncogene. Trends Biochem Sci . 1989 Oct;14(10):404-7.
- Role of proto-oncogene activation in carcinogenesis. Environ Health Perspect . 1992 Nov;98:13-24.
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Genetic Disorders: Definition, Cause, Symptoms, and Examples
Continue ReadingWhat are Genetic Disorders?
Genetic disorders are type of biological inheritance which follows the principles that have been proposed by Gregor Mendel in the year 1865 and 1866.
Generally, in humans the Genetic disorders are type of genetic cause which happens due to abnormalities or defects in the genome of an individual.
These disorders are seen in an affected individual from birth and can be diagnosed and can be treatment to reduce the impact even though it cannot be cured purely.
It can also be identified the passages of traits by pedigree analysis or family tree.
This type of genetic disorders is rare, affecting one of thousand individuals.
These disorders may or may not be inherited. Inherited disorders are the ones which are passed through germ line cells, where as in non-inheritable conditions these disorders are caused due to mutations or some changes in the genetic material.
A best example for this condition is cancer, which is either caused by environmental conditions or lifestyle factors or though inherited conditions.
Principles of Genetic Disorders
The research carried out by Mendel on pea plants stands as a base for understanding all the inheritances which are characterized by a single gene disorders.
Mendelian genetic disorders are caused due to a mutation in a single gene locus, where the locus is present in autosome or allosome.
It occurs either as a dominant or a recessive allele. If the individual who is having this disorder then the pedigree analysis is followed to find whether this disorder is present in an autosome or allosome in large families then dominant and recessive condition can also be found through that.
Mendel also suggested two laws for knowing the inherited disorders better.
Law of Segregation
Mendel’s law of segregation states that at the time of formation of genes two genes are separated so that each gene will carry one of the alleles.
Law of Independence
Mendel’s law of independence states that during the time of separation of gametes, each gene pair separates independently with other pairs.
It can also be said that the allele received by the gamete for one pair is independent of the allele received for the other allele.
Types of Genetic Disorders
Genetic disorders are classified depending upon the Mendel’s law of inheritance.
It is of five types namely;
Autosomal dominant
Autosomal recessive
Sex-linked dominant
Sex-linked recessive
Mitochondrial
All these types of Mendelian disorders can be identified with the help of pedigree analysis.
Examples of Genetic Disorders
Examples of Mendelian Genetic disorders include;
Sickle cell anaemia
Muscular dystrophy
Cystic fibrosis
Thalassemia
Phenylketonuria
Colour blindness
Skeletal dysplasia
Haemophilia
Haemophilia
It is one of the types of sex-linked recessive disorder. Here, the unaffected carrier mother passes this condition to their sons.
This disorder is rare in females because they get only one gene through the parents at most of the times, so the probability will be as a carrier mother or as an unaffected one.
So, it is very rare that females will be an affected individual.
In this disorder the blood will not clot easily after an injury or any other accidents.
Males are most frequently affected to this type of disorder.
Sickle Cell Anaemia
It is one type of autosomal recessive disorder where the disorder is carried to the offspring’s if two parents are carriers of this disease.
This disorder is caused due to the mutation in the hemoglobin molecule where the glutamic acid present in the sixth position in a hemoglobin molecule in a beta chain is replaced by valine.
So, the hemoglobin molecules acquire a change in shape, by converting into a sickle shape from its normal biconcave shape which reduces the oxygen carrying capacity of the cells and this shape of molecules cannot be easily passed through the vascular system and it results in forming a block in small blood vessels such as capillaries.
Phenylketonuria
It is one of the autosomal recessive disorder caused due to the inborn error of phenylalanine metabolism which is one of the important amino acid needed for the body.
This disorder, affects the conversion of enzyme phenyl alanine into tyrosine as a result phenylalanine is being accumulated in the body which results in formation of many derivatives and causes mental retardation in most of the cases.
Thalassemia
It is one of the types of autosomal recessive disorder. In this type of disorder body makes abnormal amount of hemoglobin so it leads to a condition where higher amount of red blood cells is destroyed and causes anemia.
It causes symptoms such as abdominal swelling, dark urine excretion, deformities of facial bones etc.
Cystic Fibrosis
It is one of the types of autosomal recessive disorder where the lungs and digestive system gets affected completely and there is also a thick production or secretion of mucus which blocks the lungs and pancreas.
Usually, the person affected with this syndrome has very short life span.
Genetic Disorders Citations
- Genetic disorders. JEMS . 2014 Feb;39(2):64-71.
- Developmental Support for Infants With Genetic Disorders. Pediatrics . 2020 May;145(5):e20190629.
- Genetic disorders of nuclear receptors. J Clin Invest . 2017 Apr 3;127(4):1181-1192.
- Genetic Disorders of the Extracellular Matrix. Anat Rec (Hoboken) . 2020 Jun;303(6):1527-1542.
- Coatopathies: Genetic Disorders of Protein Coats. Annu Rev Cell Dev Biol . 2019 Oct 6;35:131-168.
- Maternal Genetic Disorders in Pregnancy. Obstet Gynecol Clin North Am . 2018 Jun;45(2):249-265.
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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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