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Displaying molecules using a skeletal representation The skeletal representation makes use of the fact that carbon and hydrogen are the most common elements in organic compounds, and also that carbon almost always forms four covalent bonds. (A) The process of converting a displayed formula into a skeletal formula has three stages: (i) the molecule is drawn with the carbon chain 'staggered' in a zigzag; this is important to allow correct identification of the number of carbon atoms in the final molecule and is a better representation of the actual bond angles. (ii) The 'C' label for carbon atoms is omitted. (iii) The 'H' label for hydrogen atoms is omitted only for hydrogen atoms bonded to carbon. When interpreting a skeletal formula, we assume that carbon will make four bonds; if a carbon appears to make fewer than four bonds in the skeletal representation, then the 'missing' bonds are assumed to be to hydrogen atoms. Using the skeletal representation highlights the heteroatoms present in the molecule and becomes particularly useful once we consider how to display different isomers. (B) The guidelines for drawing skeletal structures are relatively flexible and in some cases, for example where we wish to draw attention to a particular group of atoms, the 'C' symbol for some of the carbon atoms may be shown. It is important not to omit any hydrogen atoms bonded to carbon atoms that are explicitly displayed in this way. (C) Wedge and hashed bonds can be used to illustrate the direction of bond vectors relative to the plane of the page.
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Within every living organism, countless reactions occur every second. These reactions typically occur more rapidly and with greater efficiency than would be possible under the same conditions in the chemical laboratory, and while using only the subset of elements that are readily available in nature. Despite these apparent differences between life...
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Context 1
... groups have a characteristic chemical behaviour, and it is possible to pre- dict some of the properties of a molecule based on which functional groups are present. When discussing organic compounds we will use the skeletal representation; those unfamiliar with this representation should refer to Figure 5. Functional groups that are commonly found in biological molecules are shown in Figure 6. ...
Citations
... Proteins are organic molecules composed of carbon, hydrogen, nitrogen, oxygen, and sulfur [1][2][3][4][5]. The core carbon atom is coupled to a side chain group, an amine group, a carbonyl group, and a hydrogen atom [6] to form a protein molecule. ...
Protein molecules show varying degrees of flexibility throughout their three-dimensional structures. The flexibility is determined by the fluctuations in torsion angles, specifically phi (φ) and psi (ψ), which define the protein backbone. These angle fluctuations are derived from variations in backbone torsion angles observed in different models. By analyzing the fluctuations in Cartesian coordinate space, we can understand the structural flexibility of proteins. Predicting torsion angle fluctuations is valuable for determining protein function and structure when these angles act as constraints. In this study, a machine learning method called TAFPred is developed to predict torsion angle fluctuations using protein sequences directly. The method incorporates various features, such as disorder probability, position-specific scoring matrix profiles, secondary structure probabilities, and more. TAFPred, employing an optimized Light Gradient Boosting Machine Regressor (LightGBM), achieved high accuracy with correlation coefficients of 0.746 and 0.737 and mean absolute errors of 0.114 and 0.123 for the φ and ψ angles, respectively. Compared to the state-of-the-art method, TAFPred demonstrated significant improvements of 10.08% in MAE and 24.83% in PCC for the phi angle and 9.93% in MAE, and 22.37% in PCC for the psi angle.
... The body of organisms is constructed with blend of different elements. Some chemical elements like carbon, hydrogen, oxygen and nitrogen are able to produce biological macromolecules which are vital for biochemical reactions and physiological functions in the organisms, and these organic biomolecules are the fundamental components of carbohydrates, protein, lipid and nucleic acid (Jonsson et al. 2017). Other groups of elements are minerals, or essential trace elements are important with certain daily magnitudes, any deficiency in these required elements could develop disorders that could lead to death. ...
Exposure to Lead (Pb 2+) in its organic and inorganic forms is known to have deleterious effects on the health of individuals. Several studies showed that these effects are due to accumulation in vital organs and induction of oxidative stress. This study examines the possibility of three different antioxidant substances (Aqueous garlic extract, Vitamin C and Vitamin E-Selenium) to act as chelating agents against organolead toxicity (lead acetate) by decreasing its accumulation in liver and spleen. To achieve this purpose, forty-eight adult male albino rats were divided into eight equal groups; Group I: Control received normal water, Group II: received lead acetate (100 mg/kg/day; i.p), Group III: received garlic (100 mg/kg; orally), Group IV: received Lead (100 mg/kg/day; i.p) + Garlic (100 mg/kg; orally), Group V: received Vitamin C (100 mg/kg; orally), Group VI: received Lead (100 mg/kg/day; i.p) + Vitamin C (100 mg/kg; orally). Group VII: received Vitamin E (100 mg/kg; orally) + Selenium (0.5 mg/kg; orally) and Group VIII: received Lead (100 mg/kg/day; i.p) + Vitamin E (100 mg/kg; orally) + Selenium (0.5 mg/kg; orally). The experiments were performed over four consecutive weeks, after which blood was withdrawn from rats by heart puncture and animals were sacrificed by cervical dislocation; the liver and spleen were removed to quantify their lead content by Flame Atomic Absorption Spectroscopy (FAAS). Analysis of the serum showed that lead acetate has significantly elevated the activity of the ALT, AST, and LDH compared to the control group, and the three selected antioxidant substances were able to minimize the activity of these enzymes significantly in comparison with lead acetate group. In addition, the results from the FAAS showed that lead concentration has significantly increased in the liver and spleen of the lead acetate group compared to the control group, and that treatment with antioxidants was not effective in reducing that effect. It is concluded that the selected antioxidants had an ameliorative effect against the hepatotoxicity induced by lead acetate but could not be considered the suitable heavy metal chelator to overcome the bioaccumulated lead in the vital organs.
... This is particularly important since carbon is considered as the source of life from many aspects. The bio-applicability along with the properties inherited from the carbonic structure enables various opportunities for biological applications to these tiny, nanoscale particles [4][5][6][7]. GQDs are semiconductor nanomaterials that belong to the carbon quantum dots family [8], they display superior photo stability against blinking and photo bleaching [9], possess low toxicity, high biocompatibility [10], and good colloidal stability [11]. Owing to quantum confinement and edge effects, GQDs are holding extraordinary properties and attracting extensive attention [12]. ...
Graphene quantum dots (GQDs) are considerably a new member of the carbon family and shine amongst other members, thanks to their superior electrochemical, optical, and structural properties as well as biocompatibility features that enable us to engage them in various bioengineering purposes. Especially, the quantum confinement and edge effects are giving GQDs their tremendous character, while their heteroatom doping attributes enable us to specifically and meritoriously tune their prospective characteristics for innumerable operations. Considering the substantial role offered by GQDs in the area of biomedicine and nanoscience, through this review paper, we primarily focus on their applications in bio-imaging, micro-supercapacitors, as well as in therapy development. The size-dependent aspects, functionalization, and particular utilization of the GQDs are discussed in detail with respect to their distinct nano-bio-technological applications.
... The properties of collagen are dictated by the peptide bond. The carbonyl oxygen of peptide has a negative charge, while the amide nitrogen with a positive charge, thus establishing a small electric dipole [21]. When collagen is mechanically deformed, electric charges are produced, and the electrical potential generated promotes bone growth and regeneration [22][23][24][25][26]. ...
Polyvinylidene fluoride (PVDF) and polyvinylidene fluoride-trifluoroethylene (P(VDF-TrFE) with excellent piezoelectricity and good biocompatibility are attractive materials for making functional scaffolds for bone and neural tissue engineering applications. Electrospun PVDF and P(VDF-TrFE) scaffolds can produce electrical charges during mechanical deformation, which can provide necessary stimulation for repairing bone defects and damaged nerve cells. As such, these fibrous mats promote the adhesion, proliferation and differentiation of bone and neural cells on their surfaces. Furthermore, aligned PVDF and P(VDF-TrFE) fibrous mats can enhance neurite growth along the fiber orientation direction. These beneficial effects derive from the formation of electroactive, polar β-phase having piezoelectric properties. Polar β-phase can be induced in the PVDF fibers as a result of the polymer jet stretching and electrical poling during electrospinning. Moreover, the incorporation of TrFE monomer into PVDF can stabilize the β-phase without mechanical stretching or electrical poling. The main drawbacks of electrospinning process for making piezoelectric PVDF-based scaffolds are their small pore sizes and the use of highly toxic organic solvents. The small pore sizes prevent the infiltration of bone and neuronal cells into the scaffolds, leading to the formation of a single cell layer on the scaffold surfaces. Accordingly, modified electrospinning methods such as melt-electrospinning and near-field electrospinning have been explored by the researchers to tackle this issue. This article reviews recent development strategies, achievements and major challenges of electrospun PVDF and P(VDF-TrFE) scaffolds for tissue engineering applications.
The surface-bulk partitioning of small saccharide and amide molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80 Å cubic water box containing a series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water bulk were examined at a molecular level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars and amides leads to the migration of the molecule toward the interface. Within the first 2 nm from the water surface, surface-active solutes lose their rotational freedom and adopt a preferred orientation with the alkyl group pointing toward the surface. The different packing within the interface leads to different solvation shell structures and enhanced interaction between the organic molecules and absorbed OH radicals. The simulations provide quantitative information about the dimension, composition, and organization of the air-water interface as well as about the nonreactive interaction of the OH radicals with the organic solutes. It suggests that increased concentrations, preferred orientations, and decreased solvation near the air-water surface may lead to differences in reactivities between surface-active and surface-inactive molecules. The results are important to explain how heterogeneous oxidation mechanisms and kinetics within interfaces may differ from those of the bulk.
Structural biology is the study of the molecular arrangement and dynamics of biological macromolecules, particularly proteins. The resulting structures are then used to help explain how proteins function. This article gives the reader an insight into protein structure and the underlying chemistry and physics that is used to uncover protein structure. We start with the chemistry of amino acids and how they interact within, and between proteins, we also explore the four levels of protein structure and how proteins fold into discrete domains. We consider the thermodynamics of protein folding and why proteins misfold. We look at protein dynamics and how proteins can take on a range of conformations and states. In the second part of this review, we describe the variety of methods biochemists use to uncover the structure and properties of proteins that were described in the first part. Protein structural biology is a relatively new and exciting field that promises to provide atomic-level detail to more and more of the molecules that are fundamental to life processes.
