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Reading an amino acid physicochemical properties diagram

Reading an amino acid physicochemical properties diagram


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I want to know if I am reading the venn diagram correctly and why there are discrepancies in the diagrams.

I'm trying to determine which amino acids are considered hydrophobic and I am using this diagram suggested by my teacher from Amino acid properties and consequences of subsitutions.

From the diagram I've determined that A, G, C, T, V, I, L, F, W, Y, H, K, M are hydrophobic.

My problem is when I visit other sources I do not get the same results. Using Amino Acid Table I determines that A, G, I, L, M, F, P, W, Y, V were hydrophobic:

Furthermore, there is even another different venn diagram from Decoding the Building Blocks of Life from the Perspective of Quantum Information


Polarity and hydrophobicity are not discrete phenomena and, therefore, categorizing amino acids as such has some measure of arbitrariness, especially at edge cases. It all depends on one's definition.

Other properties have similar problems. Charge depends on pH. And what is the cut-off between “large” and “medium” sides chains?

What is, in my opinion, more important than memorizing charts/diagrams/etc (unless you have an exam) is understanding why different amino acids have these properties. For example, why can threonine or tyrosine be classified as both hydrophobic and polar? Why can cysteine or serine, which are classified as uncharged, act as strong nucleophiles in enzymatic reactions?


Comparison of Amino Acids Physico-Chemical Properties and Usage of Late Embryogenesis Abundant Proteins, Hydrophilins and WHy Domain

Late Embryogenesis Abundant proteins (LEAPs) comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide family of proteins called hydrophilins, while a domain called WHy (Water stress and Hypersensitive response) was found in LEAP class 8 (according to our previous classification). Since little is known about hydrophilins and WHy domain, the cross-analysis of their amino acids physico-chemical properties and amino acids usage together with those of LEAPs helps to describe some of their structural features and to make hypothesis about their function. Physico-chemical properties of hydrophilins and WHy domain strongly suggest their role in dehydration tolerance, probably by interacting with water and small polar molecules. The computational analysis reveals that LEAP class 8 and hydrophilins are distinct protein families and that not all LEAPs are a protein subset of hydrophilins family as proposed earlier. Hydrophilins seem related to LEAP class 2 (also called dehydrins) and to Heat Shock Proteins 12 (HSP12). Hydrophilins are likely unstructured proteins while WHy domain is structured. LEAP class 2, hydrophilins and WHy domain are thus proposed to share a common physiological role by interacting with water or other polar/charged small molecules, hence contributing to dehydration tolerance.

Citation: Jaspard E, Hunault G (2014) Comparison of Amino Acids Physico-Chemical Properties and Usage of Late Embryogenesis Abundant Proteins, Hydrophilins and WHy Domain. PLoS ONE 9(10): e109570. https://doi.org/10.1371/journal.pone.0109570

Editor: Joshua B. Benoit, University of Cincinnati, United States of America

Received: May 21, 2014 Accepted: September 7, 2014 Published: October 8, 2014

Copyright: © 2014 Jaspard, Hunault. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.

Funding: This work was supported by a grant from Université d'Angers “Découverte de motifs souples au sein de classes de protéines intrinsèquement non structurées ou pleinement structurées”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.


Lipids: Types and Chemical Properties (With Diagram)

Let us make an in-depth study of the types and chemical properties of lipids. The three types of lipids are: (A) Simple Lipids (B) Compound Lipids (C) Derived Lipids and chemical properties of lipids are: 1. Saponification 2. Saponification Number 3. Iodine Number and 4. Rancidity.

Types of Lipids:

(A) Simple Lipids:

They are esters of fatty acids with alcohol. Depending upon the alcohol, they are further classified as:

These are esters of fatty acids with glycerol (a trihydric alcohol). These are known as triacylglycerol’s (TAG) or triglycerides.

R1, R2, and R3 are the three fatty acids. All the three may be the same or different. If all the three Rs are the same, then it may be, Tripalmitin-3 palmitic acids esterified with glycerol. Tristearin-3 stearic acids esterified with glycerol. If the ‘R’ groups are different then it is spelled out as Palmito-stearo-olein indicating that glycerol is esterified with palmitic acid, stearic acid and oleic acid.

These are esters of long chain fatty acids with long chain alcohol, e.g., Bee wax is ester of oleic acid (18 carbons) and oleyl alcohol (18 carbons).

(B) Compound Lipids:

Simple lipids in combination with some other group are called compound lipids.

Depending upon the group attached (prosthetic group) the compound lipids are further classified as:

They contain a phosphoric acid as the prosthetic group.

Depending upon the alcohol present they are further classified as:

(a) Glycerophospholipids:

They contain the alcohol-glycerol. The components of glycerophospholipids are glycerol, two fatty acids (the one at α-position is saturated fatty acid and the other at β-position is unsaturated), phosphoric acid and a base. Glycerol, fatty acids and phosphate together form a phosphatide to which a base is attached. Depending upon the base present there are various glycerophospholipids.

Phophatidyl choline or lecithin:

Phosphatidyl ethanolamine or cephalin:

Here the base is ethanol amine, attached through — OH group.

Here the base is the amino acid serine.

Phosphatidyl inositol:

Here the base is inositol.

Here one of the fatty acids of the phosphatide is replaced by a long chain aldehyde which is in an enolic form. The base may be choline or ethanolamine.

Cardiolipin or di-phosphatidyl glycerol:

Here two phosphatide groups are linked together through a glycerol.

(b) Sphingophospholipids:

These phospholipids have sphingol as the alcohol. Sphingol is an amino alcohol with a chain length of 18 carbons having a double bond at trans delta 4 position. An example of sphingophospholipid or sphingolipid is sphingomyelin, which contains a fatty acid at the amino group (and this combination, i.e., sphingol and fatty acid is known as ceramide), a phosphoric acid at the primary alcohol and the base choline is attached to this phosphate group.

These lipids contain a carbohydrate attached to the sphingol at the primary alcohol. They are also known as glycosphingosides or cerebrosides.

(a) Glucocerebrosides:

If the sugar is glucose, then they are called as glucocerebrosides.

(b) Galactocerebrosides:

If the sugar is galactose then they are called as galactocerebrosides.

These are complex sphingolipids made up of several sugar units, viz., glucose, galactose, galactosamine and N-acetyl-neuramic acid or sialic acid.

These are lipids in conjugation with proteins. They mainly function for the transport of lipids (hydrophobic) through the blood (hydrophilic).

The different types of lipoproteins and their composition is:

These lipoproteins are classified depending upon their densities in water. The density of a lipoprotein depends upon the fat content of that lipoprotein, more the fat content lower the density and hence it floats on the surface of water (vice versa). The protein part in the lipoprotein is known as apoprotein. The various types of apoproteins found in lipoproteins are apoprotein- A, B, C, D, E. Lipoproteins also constitute the combination of membrane proteins with membrane lipids.

(C) Derived Lipids:

These are the compounds obtained on hydrolysis of simple and compound lipids. They also constitute all those compounds that are related to fatty acids. They include fatty acids, steroids, eicosanoids (prostanoids- prostaglandins, prostacyclins, thromboxanes-leukotrienes and lipoxins), carotenoids, etc.

All compounds containing the cyclo-pentano-perhydro-phenanthrene ring are called steroids. The most abundant steroids in the human body are the sterols, i.e., an alcohol (—OH) group is attached to the steroid nucleus, e.g., cholesterol, ergosterol, bile acids, sex hormones, adrenal cortical hormones and vitamin D3.

Cholesterol is the major sterol in the body. It is a constituent of cell membrane and provides rigidity to it. Cholesterol acts as the precursor for all the other steroids in the body, viz., testosterone, estrogen, progesterone, vitamin-D, bile salts, corticosteroids, etc.

They are the derivatives of polyunsaturated fatty acids, mainly the arachidonic acid (C20) or even linoleic acid (C18). They are 20 carbon fatty acids with a 5 membered ring.

There are four types of prostaglandins PGE, PGF, PGA and PGB. But only PGE and PGF are important. The E group of prostaglandins contains a keto group at C-9, two -OH groups at C-11 and C-15 positions. The various types of PGE are E1, E2, E3.

The PGF groups contain -OH group at all the three positions. The various types of PGF are F1, F2 and F3. Among the subtypes there are two more sub-subtypes in each of the prostaglandins, i.e., α and β.

Functions of Prostaglandins:

Prostaglandins are synthesized in all tissues and cells except RBC. They act as local hormones and are destroyed immediately.

Other functions include as under:

1. They act as vasopressors and hence lower the blood pressure.

2. They are used in induction of labour, termination of pregnancy and prevention of conception.

3. They facilitate fertilization of the ovum.

4. They are used in the treatment of gastric ulcers, as they diminish HCl secretion.

5. They are used to prevent inflammation.

6. They are used in asthma and congenital heart diseases.

7. They promote platelet aggregation (after conversion to thromboxane’s).

8. PGE2 acts as a messenger between hormone receptor and adenylate cyclase enzyme.

Chemical Properties of Lipids:

1. Saponification:

Hydrolysis of TAG with KOH or NaOH is called saponification or soap formation. These soaps are the household soaps. Sodium soaps are hard and potassium soaps are soft. Detergents have acidic group like sulphuric acid attached to the fatty acids.

2. Saponification Number:

It is the number of milligrams of KOH required to saponify the free and combined fat in 1 gram of a given fat. A high saponification number indicates that the fat is made up of low molecular weight fatty acids and vice versa.

3. Iodine Number:

It is the grams of iodine required to saturate 100 grams of fat. It is an indication of unsaturation.

4. Rancidity:

Fats contaminated with enzymes like lipase undergo partial hydrolysis and oxidation of unsaturated fatty acids at the double bonds. This is even brought about by the atmospheric moisture and temperature. Due to this, there is release of hydrogen peroxide giving a bad odour and taste to the fat. This fat is said to be rancid and the process is known as rancidity. Rancidity can be prevented by antioxidants like vitamin E, vitamin C, phenols, hydroquinone’s, etc.

Molecular structure of a cell membrane:

Each cell and sub-cellular organelles are surrounded by a lipid bi-layer. 70 to 80 per cent are polar lipids and the remainder is mostly protein. The lipid part of the membrane is polar or amphipathic lipid largely phosphoglycerides, some amounts of sphingolipids and a negligible amount of triacylglycerol’s. Cholesterol and cholesterol esters are also present in the membrane.

Membranes are very thin from 6 to 9 nm, flexible and fluid. They are freely permeable to water but impermeable to electrically charged ions like Na + , CI – or H + and to polar but uncharged molecules like sugars. These impermeable substances are transported with the help of membrane transport proteins. On the other hand lipid soluble molecules readily pass through membranes.


Physico-Chemical Properties of Nucleic Acids

In this article we will discuss about the physico-chemical properties of nucleic acids.

The size of nucleic acids varies immensely. The smallest ribonucleic acids are the tRNAs which comprise about 80 nucleotides their molecular weight is about 30 000. Ribosomal ribonucleic acids are larger they contain several thousands of nucleotides and their molecular weight can exceed 1 million.

The RNA of the tobacco mosaic virus has about 6 500 nucleotides, which corresponds to a molecular weight greater than 2 million the polycistronic messenger ribonucleic acids have comparable dimensions.

Deoxyribonucleic acids are much larger. A small DNA like the circular single-stranded DNA of phage ϕ X 174 already has 5.5 X 10 3 nucleotides and a molecular weight of 1.7 million, but that of the phage T2 comprises 2 x 10 5 pairs of nucleotides which corresponds to a molecular weight of 130 million.

The chromosome of E.coli is a circular double-stranded molecule comprising about 4 x 10 6 pairs of nucleotides its molecular weight is therefore of the order of 2 to 3 x 10 9 . In fact, the extraction of intact DNA molecules (from bacterial, plant or animal cells) is a rather delicate operation cleavages occur easily and in the past, one often attributed molecular weights much lower than the real ones.

Cells of eucaryotes have a variable number of chromosomes according to the species. Each chromosome seems to consist of only one molecule of DNA (containing about 10 8 pairs of nucleotides), associated with basic proteins, the histones, to form chromatin, consisting of a flexible chain of repetitive units, the nucleosomes.

The nucleosome, the fundamental packing unit of the DNA, contains about 200 pairs of nucleotides coiled around a nucleus consisting of 8 molecules of histones. The nucleosomal chain is itself folded up in such a manner that finally, the length of a metaphasic chromosome is about 8000 times shorter than that of the DNA it contains. Non-histone proteins (called “acid”) are also attached to the chromatin. Some of them most probably play a role in the regulation of the genetic expression at the transcrip­tional level.

On the other hand, it must be noted that the deoxyribonucleic acids found in cellular organelles (mitochondria, chloroplasts) differ by their size and base sequence from the nuclear DNA present in the same cell.

The molecular weights of deoxyribonucleic acids are determined either upon the observation of molecules by electron microscopy (it is estimated that a length of 1 μ corresponds to a molecular weight of 10 6 for a single-stranded structure, or 2 x 10 6 for a double-stranded structure), or from the sedimenta­tion constant of the DNA, obtained by comparing its rate of sedimentation in sucrose gradient (from 5 to 20%) to that of a DNA of known sedimentation constant. (Then, with the help of an empirical equation, the molecular weight is calculated from the value of S).

Very often, for preparative of analytical purposes, one uses the sedimentation equilibrium in a CsCl gradient established during the centrifugation this gives a density gradient ranging generally from 1.65 to about 1.75 g/ml.

The DNA is concentrated in a band at the place where the density of CsCl solution is equal to its own and this density is generally determined by comparison with a DNA of known density, centrifuged in the same gradient. The density of a DNA at the sedimentation equilibrium increases with greater percentages of G-C pairs of the DNA (because G-C pairs are more dense then A-T pairs).

The DNA solutions have a very high viscosity due to the considerable length and relative rigidity of the double helix. The denaturation of DNA molecules can be followed up with the help of viscosity measurements.

On the other hand, due to the presence of purine and pyrimidine bases, they absorb in ultra-violet light (just like the RNA solutions) with a maximum around 260 nm. When a solution of native DNA is heated one observes a decrease of viscosity, and an increase of it optical density (O.D.) at 260 nm (between 30 and 40%). This phenomenon is called hyperchromia effect or hyperchromicity.

It is due to the separation of the 2 strands of the double helix (spoken of as the melting of DNA), by rupture of the interchain hydrogen bonds, and since the G ≡ C bonds are stronger then the A = T bonds, the higher the GC content of a DNA, the higher will be its melting point. The curve of O.D. as a function of temperature has a sigmoidal form.

It permits the determination of a transition point, Tm, which corresponds to the temperature at which the DNA molecules are half-denatured. A DNA whose strands are thus separated, either by heat, or under the action of other physical or chemical agents (e.g., urea) is called denatured. The DNA-passes from an ordered structure (double helix) to a disordered structure (random coil).

The DNA solution can be cooled again in 2 ways:

The 2 strands remain separated (the DNA remains denatured)

This permits a re-association of the 2 strands (the AT and GC bonds are formed again) and the initial helix is reconstituted. The DNA is thus renatured and recovers its biological properties (for example the transforming activity in the case of some bacterial deoxyribonucleic acids).


Determining amino acid scores of the genetic code table: Complementarity, structure, function and evolution

The Standard Genetic Code (SGC) table was investigated with respect to the three-dimensional codon arrangement, and all possible 24 hierarchical base partitions (4! = 24). This was done by determining the amino acid scores for each codon hierarchy in relation to the 1 st horizontal, 2 nd vertical and 3 rd horizontal sub-tables.

Marked differences were observed for the hydrophobicity and lipophilicity parameters encoded by the second base of the SGC table. The nucleotide hierarchy U < C < G < A and its complement A < G < C < U at the second base correlated best with the amino acid hydrophobicity and polarity. By contrast, the hierarchy C < G < U < A and its backwards transcript A < U < G < C at the second base were associated with the amino acid parameters of lipophilicity and accessible surface area.

No association was observed between 24 base hierarchies of the codons at the 1 st and 3 rd positions with respect to the hydropathy, polarity, lipophilicity and accessible surface area. The results imply that the second base possesses the majority of information content with respect to the physicochemical properties observed.

It is shown that amino acid information obtained by determining the scores of the bases and codon weightings in digital form coincides with physicochemical properties, and the temperature range between 25 °C and 100 °C does not affect the hydrophobicity, the related prediction of α- and β-protein structure, codon scores, or the complementarity code for sense and antisense peptide interactions.

The amino acid scores determined for the SGC table enable the construction of rules and algorithms for the analysis of the structure, function and evolution of proteins. It has been demonstrated that IUPAC-based encoding of nucleobase and amino acid sequences could be used for the representation of the bases with the Semiotic (Greimas) Square and probabilistic square of opposition.

It is concluded that the structural, functional and evolutionary patterns of the protein sequences may be modeled using codon based amino acid information, instead of using the information based on amino acid physicochemical properties only.


Table of Contents

List of Contributors
Preface
Part I The Physical Chemistry of Fundamental Biomolecules
1 Current Progress and Future Prospects of the Research on Nucleic Acids
I. Introduction
II. Nuclear Magnetic Resonance Studies
III. Experimental Evaluation of Electrostatic Interaction and Studies on Nonionic Oligonucleotide Analogues
IV. Future Prospects
References
2 The Structure of Transfer RNA Molecules in Solution
I. Introduction
II. Tertiary Structure of tRNA in Solution
III. Ring-Current Shift Theory Analysis of Low-Field nmr Spectra
IV. Hydrogen Binding of the Ribose 2'-OH Group in RNA
V. Summary
References
3 The Chemistry of Membrane-Active Peptides and Proteins
Text
References
4 Conformational Analysis of Polypeptides: Application to Homologous Proteins
I. Introduction
II. Standard Geometry
III. Computation Procedures
IV. Approaches to the Multiple-Minimum Problem
V. Computation of Models for the Three-Dimensional Structures of Three Snake Venom Inhibitors
VI. Concluding Remarks
References
5 Aspects of Biomolecules in Their Surroundings: Hydration and Cation Binding
I. Introduction
II. Hydration
III. Cation Binding
IV. The Triple System: Substrate-Water-Cation or the Problem of the Through-Water Cation Binding
References
Part II Physicochemical Aspects of the Mechanisms of Genetic Expression
6 Site-Directed Mutagenesis as a Tool in Genetics
I. Phage Qβ and Its Replication
II. Site-Directed Mutations in Qβ RNA
III. Perspectives for Site-Directed Mutagenesis
References
7 Gene Control by the λ Phage Repressor
I. Operator Structure
II. Promoter Structure
III. λ Repressor
IV. Repressor Control of Ν and cro
V. Self-Regulation of cl
VI. Translational Control of cI
VII. Summary
References
8 Nuclear Magnetic Resonance Studies of Protein-Nucleotide Interactions
I. Ternary Enzyme-Metal Nucleotide Complexes
II. Higher Enzyme-Substrate Complexes
III. Working Enzymes
IV. Conclusions
References
9 The Role of RNA's in the Structure and Function of Ribosomes
I. A Rapid Survey of Present Knowledge on the Structure of E. coli Ribosomal RNA's
II. RNA-RNA Interactions
III. Interactions between Ribosomal RNA's and Proteins
References
10 Mechanism of Initiation of Protein Synthesis
I. Initiation Sequence: Characterization of Factors
II. Selection of Initiation Signals
III. Secondary Structure of mRNA as Negative Control
IV. Part Played by Ribosomal Proteins and Initiation Factors
V. Specific Mutants Affecting Initiation
VI. Conclusion
References
Part III Biochemistry of Oxygen and Hemoglobin
11 Molecular Oxygen and Superoxide Dismutase: Environmental Threat and Biological Defense
I. Induction of Superoxide Dismutase in Escherichia coli K12
II. Induction of Superoxide Dismutase in E. coli, at Constant Oxygenation, in Response to Changes in Metabolism
III. A Convenient New Assay for Superoxide Dismutase
References
12 Indoleamine 2,3-Dioxygenase: A Superoxide-Utilizing Enzyme
I. Introduction
II. Biological Function
III. Purification and Molecular Properties
IV. Role of Superoxide Anion
V. Experiments with KO2
VI. Interaction of Enzyme with KO2
VII. Experiments with 18O2-
VIII. Interaction of Enzyme with Substrate
IX. Is O2- a Substrate in Vivo?
X. Conclusion
References
13 Reaction Intermediates of D-Amino Acid Oxidase
I. Introduction
II. Occurrence of Two Types of Oxidoreduction Intermediates
III. Lifetime of the Purple Intermediate
IV Effect of Hydrogen Bonding on the Formation of the Intermediate
V. Role of Protein in the Formation of the Intermediates
VI. Reactivity of the Intermediates with Molecular Oxygen
References
14 Biological Aspects of Superoxide Dismutase
I. Introduction
II. Production of O2-
III. Superoxide Dismutases
IV. Variation in SOD Levels during Development of Ceratitis capitata
V. Erythrocyte SOD, Catalase, and Glutathione Peroxidase Levels in Different Animals
VI. Biological Utility of O2-
VII. Toxicity of Superoxide Radicals
VIII. Ionizing Irradiations
IX. Chemiluminescence of O2-
X. Clinical Aspects of SOD Levels in Humans
XI. General Conclusion
References
15 Recent Developments on the Active-Site Structure and Mechanism of Bovine Copper- and Zinc-Containing Superoxide Dismutase
I. Chemical Structure of the Metal Binding Sites and General Reaction Mechanism of the Enzyme
II. Anionic Inhibitors of the Enzyme
III. Spectral Studies of Co2+-Substituted Superoxide Dismutase
IV. Catalytic Protonation and Deprotonation of the Bridging Imidazole
References
16 Binding of Oxygen to Hemoglobin A in the T-State
I. Models
II. The Value of L and Properties of R- and T-State Hemoglobins
III. Effects of Temperature on the Oxygen-Hemoglobin Reaction
IV. Effect of pH and Effectors
V. Conclusions and Problems
References
Part IV Study of Organized Systems
17 The Structure and Assembly of the Membrane of Semliki Forest Virus
I. Semliki Forest Virus
II. Composition of SFV
III. Growth Cycle of SFV
IV. Structure of the Virus Membrane Glycoproteins
V. The Final Event in Virus Maturation: The Budding
Process
References
18 Oscillations: A Property of Organized Systems
I. General Mechanistics of Dynamic Organization
II. Nonequilibrium Dynamics
III. Experimental Observation of Oscillations
IV. General Remarks
References
19 Cation-Induced Regulatory Mechanism of Enzyme Reactions
I. Introduction
II. Catalytic Implications of the Polyelectrolyte Theory: An Oversimplified Treatment
III. Membrane-Bound Enzymes
IV. Gene Expression Systems
V General Conclusion
References
20 The Proton Pumps of Photosynthesis
I. Introduction
II. Protolytic Reactions in Green Plant Photosynthesis
III. The Proton Pumps of Bacterial Photosynthesis
IV. Photochemical Reaction Centers
References
21 The Photosynthetic Intramembrane Electric Field
I. Formation of the Membrane Potential in Algae
II. Relaxation of the Membrane Potential
References
Subject Index


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AVAILABILITY

The AAindex database can be retrieved through the DBGET/LinkDB system ( 14 ) of the Japanese GenomeNet service ( 15 ) at http://www.genome.jp/dbget-bin/www_bfind?aaindex .

The DBGET/LinkDB system integrates most of the major molecular biology databases and is especially suited for using hyperlinks to related entries within the AAindex database as well as to the other databases. Alternatively, the entries database may be copied and used locally. The URL for anonymous FTP is: ftp://ftp.genome.jp/pub/db/community/aaindex/

BioRuby that is a bioinformatics library of Ruby programming language has provided the useful functions to handle the AAindex database ( http://bioruby.org/ ). EMBOSS ( 16 ) has provided a program to extract the index data from the AAindex entry.

Users are requested to cite this article when making use of the AAindex database.


Conclusions

The results showed that i) the E+K/Q+H values for proteome discriminated organisms according their OGT: >4.5 for HT 3.2 to 4.6 for T <2.5 for ME ii) the high percent of E and K associated to the low % of H and Q could be related to protein thermostability iii) the AGR codon bias for Arg can be used as a signature for HT and T iv) the E+K/Q+H ratio and codon bias for Arg are not apparently related to phylogeny. Members HT of the Bacteria domain show the same values as the HT members of the Archaea domain the values for T organisms are related to their lifestyle (intermediate temperature) and not to their domain (Archaea) and the values for M are similar in Eukarya, Bacteria and Archaea.


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DNA structure and function

The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase.

Keywords: A-DNA B-DNA DNA as an energy store DNA backbone conformation DNA elasticity DNA information DNA structure DNA topology alternative DNA structures genome organisation.


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