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Is hydroxyproline an amino acid? (Classification question)

Is hydroxyproline an amino acid? (Classification question)


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So I know that hydroxyproline is created from proline via hydroxylation as a post-translational modification. I also know that proline is considered an amino acid. However, once you hydroxylize it, you have made a covalent modification to the original amino acid. Can hydroxyproline be correctly considered an amino acid? Or is it simply an amino acid derivative and NOT an amino acid?

Or, a more general question - how much can you change an amino acid and still call it an amino acid?


The other commenter answered correctly that proline is an imminoacid, not an amminoacid. But in biochemistry it is referred to as amminoacid since it basically works like every other amminoacid in any polypeptyde.

how much can you change an amino acid and still call it an amino acid?

Have a look at:

As you can see there are some weird modifications of amminoacids in biology. Just like proline/hydroxyproline any amminoacid can be very well modified and be used in proteinogenesis or non-proteinogenesis. Every modification of an amminoacid is allowed, and it will still be considered an amminoacid, even if it doesn't make up a protein. The only parts which can't be changed are the COO- and NH3+ groups, obviosuly, since they give the name of the molecule: "ammino" means that it has a NH group and "acid" means it has a COO- group.


Amino Acids Classification and its Basics

In this article, we are adding Amino acids Classification details.

Amino acids are the building blocks of the molecular structure of the important and complex class of a compound known as Proteins.

The proteins on hydrolysis yield mixtures of the component amino acids.

Therefore, to understand the structure and chemistry of proteins, we have to first undertake the study of amino acids.


Classification

In addition to the amino and carboxyl groups, amino acids have a side chain or R group attached to the &alpha-carbon. Each amino acid has unique characteristics arising from the size, shape, solubility, and ionization properties of its R group. As a result, the side chains of amino acids exert a profound effect on the structure and biological activity of proteins. Although amino acids can be classified in various ways, one common approach is to classify them according to whether the functional group on the side chain at neutral pH is nonpolar, polar but uncharged, negatively charged, or positively charged. The structures and names of the 20 amino acids, their one- and three-letter abbreviations, and some of their distinctive features are given in Table (PageIndex<1>).

Table (PageIndex<1>): Common Amino Acids Found in Proteins
Common Name Abbreviation Structural Formula (at pH 6) Molar Mass Distinctive Feature
Amino acids with a nonpolar R group
glycine gly (G) 75 the only amino acid lacking a chiral carbon
alanine ala (A) 89 &mdash
valine val (V) 117 a branched-chain amino acid
leucine leu (L) 131 a branched-chain amino acid
isoleucine ile (I) 131 an essential amino acid because most animals cannot synthesize branched-chain amino acids
phenylalanine phe (F) 165 also classified as an aromatic amino acid
tryptophan trp (W) 204 also classified as an aromatic amino acid
methionine met (M) 149 side chain functions as a methyl group donor
proline pro (P) 115 contains a secondary amine group referred to as an &alpha-imino acid
Amino acids with a polar but neutral R group
serine ser (S) 105 found at the active site of many enzymes
threonine thr (T) 119 named for its similarity to the sugar threose
cysteine cys (C) 121 oxidation of two cysteine molecules yields cystine
tyrosine tyr (Y) 181 also classified as an aromatic amino acid
asparagine asn (N) 132 the amide of aspartic acid
glutamine gln (Q) 146 the amide of glutamic acid
Amino acids with a negatively charged R group
aspartic acid asp (D) 132 carboxyl groups are ionized at physiological pH also known as aspartate
glutamic acid glu (E) 146 carboxyl groups are ionized at physiological pH also known as glutamate
Amino acids with a positively charged R group
histidine his (H) 155 the only amino acid whose R group has a pKa (6.0) near physiological pH
lysine lys (K) 147 &mdash
arginine arg (R) 175 almost as strong a base as sodium hydroxide

The first amino acid to be isolated was asparagine in 1806. It was obtained from protein found in asparagus juice (hence the name). Glycine, the major amino acid found in gelatin, was named for its sweet taste (Greek glykys, meaning &ldquosweet&rdquo). In some cases an amino acid found in a protein is actually a derivative of one of the common 20 amino acids (one such derivative is hydroxyproline). The modification occurs after the amino acid has been assembled into a protein.


NET Life Science Model Question Paper 2015: Biology MCQ-8: Biochemistry: Amino Acids: Part 4

1). Which group of a fully protonated glycine (NH3+ – CH2 – COOH) first release a ‘proton’ when it is titrated against – OH- ions?
a. Carboxyl group
b. Amino group
c. Both at the same time
d. It cannot be predicted

2). pKa is the measure of a group to __________ proton.
a. Take up
b. Release
c. Combine
d. Consume

3). Which of the following amino acid bears a guanidine group in the side chain?
a. Lysine
b. Arginine
c. Histidine
d. Proline

4). The precursor of glycine synthesis in microbes and plants is_______.
a. Serine
b. Leucine
c. Valine
d. None of these

5). Single letter code of selenocysteine is _____.

6). Which of the following amino acid have an imino group in the side chain?
a. Proline
b. Asparagine
c. Glutamate
d. Histidine

7). 4-hydroxy proline (a derivative of proline) is abundantly present in _______.
a. Keratin
b. Myoglobin
c. Hemoglobin
d. Collagen

Biology MCQ-8: Biology/Life Science Multiple Choice Questions (MCQ) / Model Questions with answers and explanations in Biochemistry: Amino Acids Part 4 for preparing CSIR JRF NET Life Science Examination and also for other competitive examinations in Life Science / Biological Science such as ICMR JRF Entrance, DBT JRF, GATE Life Science, GATE Biotechnology, ICAR, University PG Entrance Exam, JAM, GRE, Medical Entrance Examination etc. This set of practice questions for JRF/NET Life Science will help to build your confidence to face the real examination. A large quantum of questions in our practice MCQ is taken from previous year NET life science question papers. Please take advantage of our NET Lecture Notes , PPTs , Previous Year Questions and Mock Tests for you preparation. You can download these NET study material for free from our Slideshare account (link given below).

8). Desmosine is a complex derivative of five ____________ residues.
a. Lysine
b. Arginine
c. Histidine
d. Methionine

9). Isoelectric pH is designated as______.
a. pKa
b. pI
c. Pi
d. None of these

10). Which of the following amino acid is biosynthesized from Ribose 5-phposphate?
a. Histidine
b. Serine
c. Glycine
d. All of these

11). Amino acid biosynthesized from Pyruvate of glycolysis is _____.
a. Alanine
b. Valine
c. Leucine
d. All of these

12). Aromatic amino acids (Phenylalaine, Tyrosine, and Tryptophan) are derived from Phosphoenol pyruvate and __________.
a. Ribose 5-phosphate
b. Erythrose 4-phosphate
c. Oxaloacetate
d. α-ketoglutarate

13). Isoleucine is derived from ___________.

a. Methionine
b. Threonine
c. Lysine
d. Leucine

14). Blood clotting protein thrombin usually contain which of the following modified amino acid?

a. 4-hydroxy proline
b. 5-hydroxy lysine
c. 6-N-methyl lysine
d. γ-carboxy glutamate

15). Cysteine is not an essential amino acid in human, since we have the machinery to synthesize cysteine from other two amino acids namely _______ and serine.

a. Methionine
b. Selenocysteine
c. Citrulline
d. Hydroxyproline

16). Which of the following contain a disulfide bridge?

a. Cysteine
b. Cystine
c. Methionine
d. None of these
e. All of these

17). Which of the following protein contain a modified amino acid – desmosine?

a. Keratin
b. Gelatin
c. Elastin
d. Collagen

180. During biosynthesis, Methionine and Threonine are derived from a common intermediate:

a. Chorismate
b. Citrulline
c. Homoserine
d. Cystathione

19). 6-N-methyl lysine is a derivative of lysine, present in__________.

a. Keratin
b. Collagen
c. Myosin
d. Myoglobin

20). A common intermediate branch point in the synthesis of all aromatic amino acids such as Tryptophan, Phenylalanine and Tyrosine is _____.

a. Homoserine
b. Chorismate
c. Cystathione
d. None of these

21). Sarcosine, a ubiquitous non protenacius amino acid in animals and plants is ____.

a. N-methylglycine
b. N-methylvaline
c. N-methylserine
d. N-methylmethionine

Answers and Explanations:

1. Ans. (a). Carboxyl group

First COOH group will release H+ ions and it will combine with OH- ions to form water. Only after complete ionization of all the COOH groups, the NH3 + release H + ions.

2. Ans. (b). Release

pKa is the negative logarithm of Ka. Ka is the dissociation constant of an ionization reaction such as the ionization of acetic acid. Ka is similar to equilibrium constant of any chemical reaction and it is calculated by dividing the concentration of products divided by concentration of its reactants. Ka denotes the strength of an acid. Strong acids will have a higher value of Ka where as a weaker acid will have a lesser values of Ka. The stronger the tendency to dissociate a proton, the stronger is the acid and the lower its pKa (Since pKa is negative logarithm of Ka i.e., reciprocal of ka).

3. Ans. (b). Arginine

4. Ans. (a). Serine

6. Ans. (a). Proline

7. Ans. (d). Collagen

8. Ans. (a). Lysine

10. Ans. (a). Histidine

11. Ans. (d). All of these

12. Ans. (b). Erythrose 4-phosphate

13. Ans. (b). Threonine

14. Ans. (d) γ-carboxy glutamate

15. Ans. (a). Methionine

Methionine provide sulfur

Serine provide the backbone of cysteine

16. Ans. (b). Cystine

17. Ans. (c). Elastin

18. Ans. (c). Homoserine

19. Ans. (c). Myosin

20. Ans. (b). Chorismate

21. Ans. (a). N-methylglycine

The answer key is prepared with best of our knowledge.
Please feel free to inform the Admin if you find any mistakes in the answer key..


Classifications of Amino Acids

Experts classify amino acids based on a variety of features, including whether people can acquire them through diet. Accordingly, scientists recognize three amino acid types:
1. Nonessential
2. Essential
3. Conditionally essential

However, the classification as essential or nonessential does not actually reflect their importance as all 20 amino acids are necessary for human health.

Eight of these amino acids are essential (or indispensable) and cannot be produced by the body. They are:
&bull Leucine
&bull Isoleucine
&bull Lysine
&bull Threonine
&bull Methionine
&bull Phenylalanine
&bull Valine
&bull Tryptophan

Histidine is an amino acid that is categorized as semi-essential since the human body doesn't always need it to properly function therefore dietary sources of it are not always essential. Meanwhile, conditionally essential amino acids aren't usually required in the human diet, but do become essential under certain circumstances.

Finally, nonessential amino acids are produced by the human body either from essential amino acids or from normal protein breakdowns. Nonessential amino acids include:
&bull Asparagine
&bull Alanine
&bull Arginine
&bull Aspartic acid
&bull Cysteine
&bull Glutamic acid
&bull Glutamine
&bull Proline
&bull Glycine
&bull Tyrosine
&bull Serine

An additional amino acids' classification depends upon the side chain structure, and experts recognize these five as:
&bull Cysteine and Methionine (amino acids containing sulfur)
&bull Asparagine, Serine, Threonine, and Glutamine (neutral amino acids)
&bull Glutamic acid and Aspartic acid (acidic) and Arginine and Lysine (basic)
&bull Leucine, Isoleucine, Glycine, Valine, and Alanine (aliphatic amino acids)
&bull Phenylalanine, Tryptophan, Tyrosine and Histidine (aromatic amino acids)

One final amino acid classification is categorized by the side chain structure that divides the list of 20 amino acids into four groups - two of which are the main groups and two that are subgroups. They are:
1. Non-polar
2. Polar
3. Acidic and polar
4. Basic and polar

For example, side chains having pure hydrocarbon alkyl or aromatic groups are considered non-polar, and these amino acids are comprised of Phenylalanine, Glycine, Valine, Leucine, Alanine, Isoleucine, Proline, Methionine and Tryptophan. Meanwhile, if the side chain contains different polar groups like amides, acids and alcohols, they are classified as polar. It includes Tyrosine, Serine, Asparagine, Threonine, Glutamine, and Cysteine. If the side chain contains carboxylic acid, the amino acids in the acidic-polar classification are Aspartic Acid and Glutamic Acid. Furthermore, if the side chain consists of a carboxylic acid and basic-polar, these amino acids are Lysine, Arginine, and Histidine.


Discussion

A Bioinformatics Approach for Identifying HRGPs

As more plant genome sequencing projects are completed, vast amounts of biological data are being generated. Bioinformatics and in particular the BIO OHIO 2.0 program, which was recently revised and improved to provide a more rapid, reliable, and efficient method to identify proteins with biased amino acid compositions and known repetitive motifs [16, 22]. For instance, the BIO OHIO/Prot-Class program can search through over 73,000 proteins in the poplar proteomic database and identify those containing at least 50 % PAST in one minute. Using the various search criteria, we have predicted 271 HRGPs in poplar, including 162 AGPs, 60 EXTs, and 49 PRPs.

Although HRGPs were identified primarily through searching for biased amino acid compositions and repetitive motifs, the possibility that other HRGPs could be found in the poplar genome exists. Not all AGPs meet the 50 % PAST threshold, for instance, one classical AGP, PtAGP51C, contains only 49 % PAST. Similar problems exist for identifying chimeric AGPs. Because these proteins may contain only a small AGP region within a much larger sequence, they are likely to contain less than 50 % PAST. The possibility remains that other classes of chimeric AGPs or individual proteins that contain AGP-like regions exist and were not identified by the search parameters used in this study. A similar problem could exist for AG peptides that fall below the 35 % PAST cut-off or for PRPs that fall below 45 % PVKCYT.

One possible solution is to simply lower the thresholds and continue to search, but the number of false positives increases markedly as thresholds are lowered, making such searches less feasible. For instance, lowering the threshold for the AG peptide search to 30 % would identify 877 proteins compared to the 194 identified with a 35 % threshold.

In such a scenario, BLAST provides an alternative means to find additional candidate proteins. When using identified proteins as queries, BLAST is effective in finding a few related family members. For example, when using identified FLAs as queries, BLAST is capable of finding additional FLAs that don’t meet the criteria of the BIO OHIO 2.0 program. However, it is not particularly effective in finding other members of HRGP superfamily and thus could not be utilized in a comprehensive manner.

Indeed, a bioinformatics search that identifies HRGPs, especially chimeric HRGPs without also identifying a very large number of false positives remains difficult. Nevertheless, the search parameters and BLAST searches used here provide an efficient means to identify HRGPs and distinguish them from a limited number of false positive sequences. Of course, future molecular and biochemical analysis of the HRGPs predicted from this study will be necessary to validate these predictions more completely and elucidate their biological functions. Only when such work is completed will it become possible to conclusively distinguish HRGPs from false positive sequences.

HRGPs exist as a spectrum of proteins

Although HRGPs are divided into AGPs, EXTs, and PRPs, the distinction between these categories is not always clear, since many HRGPs appear to exist as members of a spectrum of proteins rather than distinct categories. Indeed, several HRGPs identified here as well as some previously identified in Arabidopsis have characteristics of multiple families and can be considered hybrid HRGPs. For instance, many of the PRPs identified here, particularly some chimeric PRPs, also contain dipeptide repeats that are characteristic of AGPs. As such, it is difficult to determine if these should be considered as AGPs, PRPs, or classified as a hybrid HRGP. Determining whether these are actually AGPs or PRPs would depend on whether the proline residues are hydroxylated and subsequently glycosylated with arabinogalactan polysaccharides, which are characteristic of AGPs. Similarly, PtEXT4 also contains large numbers of characteristic AGP repeats (Additional file 2: Figure S2). In addition, BLAST searches revealed that it is similar in sequence to AtAGP51. Given that it contains many SPPP and SPPPP repeats, it was classified as an EXT. However, there is a possibility that this protein may also be glycosylated with the addition of AG polysaccharides, in which case it could potentially be grouped as a hybrid HRGP. Another example is the novel class identified here as the PR peptides (Table 4). Although grouped here as PRPs, these short sequences (i.e., PtPRP16-31 and PtPRP37) also contain a SPPP sequence characteristic of an EXT as well as the dipeptide repeats characteristic of AGPs, particularly AP, PA, and VP (Additional file 4: Figure S4).

Other difficulties arise when chimeric HRGPs are considered. For instance, the plastocyanins range from those that contain a majority of AGP repeats and easily pass the 50 % PAST test to those that contain only a few AP, PA, SP, VP, and GP repeats to those that contain no characteristic AGP repeats. The exact cutoff between proteins that are considered chimeric AGPs and those that are simply plastocyanin proteins is difficult to determine. Again, biochemical studies would be required to examine which of the proteins are actually glycosylated to make a final determination for classification. However, all those proteins annotated here as PAGs have at least a few characteristic AGP repeats, contain a signal peptide, and most have predicted GPI membrane anchor addition sequences, all of which is consistent with the chimeric AGP designation (Additional file 1: Figure S1).

A similar situation also exists for the chimeric EXTs, such as the PERKs and LRXs. How many SPPP or SPPPP repeats are required for a protein to be considered a LRX and not simply a leucine-rich repeat (LRR) protein? Here the cutoff was arbitrarily set to at least two repeats. As such, there may be LRR proteins that contain one SPPP that are not considered here as LRXs. Another example which illustrates this classification difficulty concerns the four proteins (PtAGP70I, PtAGP71I, PtAGP72I, and PtAGP73I) which are similar to AtPRP13 based on BLAST searches. However, these four proteins also contain numerous SP and AP repeats that would be more characteristic of an AGP. Exactly how proteins such as these should be classified is certainly debatable. Indeed it is human nature to group and classify items to facilitate understanding, while Mother Nature operates without such regard.

Comparisons with previously identified poplar HRGPs

This study identified 271 poplar HRGPs (162 AGPs, 60 EXT, and 49 PRPs) in contrast to the 24 HRGPs (3 AGPs, 10 EXT, and 11 PRPs) identified by Newman and Cooper [18]. The more stringent search criteria for proline-rich tandem repeats and a less comprehensive poplar proteomic database based on EST and NCBI Non-Redundant protein sequences data from10/04/09 likely account for the fewer poplar HRGPs identified in this earlier study. In addition, homologs of the 15 FLA AGPs reported by Lafarguette et al. [20] in a Populus tremula × P. alba hybrid related to Populus trichocarpa were also identified in addition to 35 other FLAs. Thus, the present study represents the most comprehensive and detailed picture of the HRGP inventory in poplar to date.

Comparisons with Arabidopsis

Findings here allow for a comparison of the HRGPs identified in Arabidopsis to those in poplar (Table 5). For AGPs, the classical AGPs identified in poplar showed a similar number as in Arabidopsis. Specifically, 27 classical AGPs including six lysine-rich AGPs were identified in poplar, while 25 classical AGPs including three lysine-rich AGPs were identified in Arabidopsis. Among other AGPs, particularly notable is the large increase the number of FLAs, PAGs, and AG peptides in poplar compared to Arabidopsis. While 21 FLAs, 17 PAGs and 16 AG peptides were identified in Arabidopsis, 50 FLAs, 39 PAGs and 35 AG peptides are identified here in poplar. There is also a noticeable increase in the number of other chimeric AGPs in poplar compared to Arabidopsis. Here, 11 other chimeric AGPs were identified in poplar, while only 6 were found in Arabidopsis.

Among EXTs, the classical EXTs with large numbers of SPPPP repeats are markedly decreased in poplar, while similar numbers of the chimeric EXTs exist in both species. The reduction in the number of classical EXTs in poplar is dramatic and likely indicates that many EXT genes or EXT functions are dispensable in poplar, and therefore not conserved in evolution. A similar loss of EXTs has also been observed in analysis of certain monocot species [unpublished data,18]. Moreover, far fewer poplar EXTs contain putative cross-linking YXY sequences compared to Arabidopsis, and this can be largely explained by the reduced number of classic EXT sequences, which typically contain such cross linking sequences. The various chimeric EXTs, namely the LRXs/PEXs, PERKs, and FHs, are conserved in both species. Although FHs were not reported in Showalter et al. [16], a reexamination of the Arabidopsis proteome shows 6 FH sequences (AtFH1-At3g2550, AtFH5-At5g54650, AtFH8-At1g70140, AtFH13-At5g58160, AtFH16-At5g07770, and AtFH20-At5g07740) contain two or more SPPP sequences. These 6 formins are included in Table 5 and are a subset of the 21 reported formins in Arabidopsis [35]. Similar to the chimeric EXTs, the short EXTs are also conserved in Arabidopsis and poplar. The short EXTs are a particularly interesting class because EXTs are not known to have GPI membrane anchors, a feature commonly found in many AGPs and associated with proteins found in lipid rafts [36]. The finding that several of these short EXTs encode a predicted GPI-anchor sequence are conserved in poplar and Arabidopsis certainly prompts the question of what role these proteins are playing in the plant. Currently, no publications verifying their biochemical existence or examining their roles exist, but this class stands out in terms of having interesting candidates for further investigation, particularly with respect to confirming their plasma membrane localization, hydroxylation, and glycosylation.

PRPs are similar in both species with the notable exception of the PR-peptides, which is a much expanded class in poplar compared to Arabidopsis, which is now recognized to have only one PR-peptide following a reexamination prompted by this study. All of the PR-peptides in poplar are similar in sequence with most containing LPPLP repeats and having a single SPPP repeat at the C terminus, although some contained PELPK repeats. In addition, most of these PR-peptides are similar to AtPRP9 and AtPRP10 based on BLAST analysis both of these Arabidopsis proteins contain PELPK repeats as well. Indeed, AtPRP9 is quite short and similar in sequence to the PR peptides found in poplar but lacks the C terminal SPPP repeat. However, this is the only such protein found in Arabidopsis, while 30 were observed in poplar. AtPRP10 contains some similarity in sequence but is much longer than the poplar PR-peptides. Indeed, the large number of LPPLP- and PELPK- containing PR-peptides in poplar clustered respectively in two chromosomal locations indicates that these two gene subfamilies likely result from tandem gene duplication events, analogous to a unique, clustered set of PEHK-containing PRP genes in the grape family [18].

Although most sub-families of HRGPs exist in both the Arabidopsis and poplar inventories, certain species-specific differences do exist, which is reflected in the difference of number of certain groups and the total number of HRGPs (271 in poplar versus 168 in Arabidopsis). Precisely why certain classes of HRGPs are increased or decreased in abundance in a particular species remains to be determined, but these results lay the groundwork for future experimentation in this area.

Poplar HRGPs genome 2.0 release and expression analysis

The study revealed that the poplar genome 3.0 release is quite different from 2.0 release in terms of HRGPs. Only 33 % of HRGPs identified in 3.0 are the same as counterparts in 2.0, others may differ from a few amino acids in sequence to a distinct start and/or stop position. For several such cases, a green highlight indicated a likely signal sequence placed internally, either because these signal sequences were at the N terminus in the 2.0 release or they should be at N terminus based on analysis of sequences in this study.

In addition, tissue/organ-specific HRGP expression data were obtained from the poplar eFP browser. However, this database does not contain all HRGP data, and it only accepts query IDs in poplar genome version 2.0 format. Judging from the available information, one could observe that HRGPs in general have high expression in seedlings, leaves, and reproductive tissues (Tables 2, 3, and 4). In particular, a number of FLAs were specifically expressed in xylem, while some PAGs were found to be highly expressed in male catkins. Many PRPs have high expression in seedlings and leaves. Interestingly, several LRXs are found to be uniquely expressed in male catkins this finding is consistent with previous research in Arabidopsis and rice that a group of LRXs are pollen-specific LRXs, or PEXs [37].

Pfam analysis of poplar HRGPs

All 271 poplar HRGPs identified in this study were subjected to Pfam analysis to identify specific domains within them. Pfam domains were found in 160 of the 271 proteins (59 %). More specifically, Pfam domains were identified in 105 of the 162 AGPs, 32 of the 62 EXTs, and 23 of the 49 PRPs. In particular, Pfam analysis exceled at finding domains within chimeric HRGPs, such as FLAs, PAGs, LRXs, PERKs, and FH EXTs. In contrast, such analysis often failed to find domains in classical AGPs or EXTs, possibly due to the variable sequences and numbers of sequence repeats associated with many of the HRGPs. Interestingly, many of the PRPs were found to contain Pollen Ole domains and Hydrophob seed domains. Pfam analysis also has merit in identifying domains in the chimeric HRGPs identified in the study. Indeed, while Pfam analysis alone is not sufficient for identifying HRGPs in a comprehensive manner, it can add valuable information to identified HRGPs, and thus a Pfam analysis module will likely be incorporated into future versions of the BIO OHIO program.


What Are "Biologics" Questions and Answers

Biological products include a wide range of products such as vaccines, blood and blood components, allergenics, somatic cells, gene therapy, tissues, and recombinant therapeutic proteins. Biologics can be composed of sugars, proteins, or nucleic acids or complex combinations of these substances, or may be living entities such as cells and tissues. Biologics are isolated from a variety of natural sources - human, animal, or microorganism - and may be produced by biotechnology methods and other cutting-edge technologies. Gene-based and cellular biologics, for example, often are at the forefront of biomedical research, and may be used to treat a variety of medical conditions for which no other treatments are available.

How do biological products differ from conventional drugs?

In contrast to most drugs that are chemically synthesized and their structure is known, most biologics are complex mixtures that are not easily identified or characterized. Biological products, including those manufactured by biotechnology, tend to be heat sensitive and susceptible to microbial contamination. Therefore, it is necessary to use aseptic principles from initial manufacturing steps, which is also in contrast to most conventional drugs.

Biological products often represent the cutting-edge of biomedical research and, in time, may offer the most effective means to treat a variety of medical illnesses and conditions that presently have no other treatments available.


Central nervous system responses to biomaterials

22.2.2.3 Collagen

Collagen is an abundant ECM protein and its presence in the natural microenvironment of the CNS has led to the extensive use and characterization of collagen as a substrate for neural tissue engineering applications. Similarly, gelatin, which is hydrolyzed collagen, has also been widely used for CNS applications. A cross-species transplantation of collagen-based scaffolds can trigger immune response for natural biomaterials like collagen. Humeral immunity is rare for type I collagen, thereby making collagen I a suitable biomaterial for implantation. A simple serological test can verify whether the patient is susceptible to an allergic reaction in response to a collagen-based biomaterial [19] . Cell–collagen interactions occur due to the loci existing on collagen-based scaffolds for the adhesion of cells and the adhesive properties of collagen can be altered by covalent modification [69–71] . The collagen-based scaffolds or gels are also highly tunable. Enhanced collagen concentration for example can increase the cell permeability rate, compressive modulus, cell number, and cell metabolic activity [20] . There have been studies that demonstrated similar physical and mechanical properties of the collagen-based scaffolds to the normal nervous tissue, suggesting excellent biocompatibility profile that can ensure successful neural tissue repair upon implantation [72,73] . Last but not least, the plastic compression of the collagen to form collagen sheet-based conduits has been very useful for PNS applications, but this technique leads to scaffolds that are probably too stiff for CNS repair therefore if such a technique is utilized for the fabrication of a collagen scaffold, the mechanical properties have to be tuned accordingly in order to match the CNS tissue characteristics as discussed by Tsintou et al. [73] .


Psychiatry Essential Reads

The Mind-and-Skin Connection

How Technology Could Progress Adolescent Psychiatry

NAC is an amino acid, something present in many foods, but supplements give you a higher dose than you’d get in your daily diet. It is usually taken in doses from 1000 to 2000 milligrams per day—usually in 600-milligram capsules taken 2 to 3 times a day, and other than mild gastrointestinal side effects NAC is usually well tolerated. [Note: Suffice it to say, you should talk to your doctor before taking this or other supplements to see whether they are suitable for you. In my psychiatric practice, I view a trial of NAC as similar to any other drug (or therapy) trial: You need to get a patient to an adequate dose for an adequate period of time, and carefully measure its effects on key symptoms (and monitor side effects) over a long enough duration to be able to conclude whether it’s helping.]

The intriguing thing about NAC to me is that it’s of great interest to neuroscience researchers. There have been many studies of this compound, including neuroimaging studies, and it has been investigated in innumerable disorders—depression, bipolar disorder, OCD, PTSD, schizophrenia, addiction, eating disorders, Alzheimer’s disease, and addiction (Berk). NAC also has established medical uses as an anti-inflammatory medicine in cases of acetaminophen overdose in preventing liver failure. Clinical trials have been promising in many (but not all) disorders where it has been studied (Berk). Clearly, there’s a need for more research studies, both more clinical trials in different disorders, and more basic research to see how NAC works in the brain.

Why does NAC help many people with psychiatric diagnoses? Why does it work across so many conditions? This is the intriguing thing, in my eyes. Are its benefits a result of its anti-inflammatory effects? Or some other mechanism? On a clinical level, in day-to-day work with patients, NAC seems to help with ruminations, with difficult-to-control extreme negative self-thoughts. Such thoughts are common in depression and anxiety disorders, and also in eating disorders, schizophrenia, OCD, etc. I’ve seen it help patients with such disorders when many other things, medicines or psychotherapies, have not helped much.

NAC doesn’t always work, but when it does, troubling irrational thoughts gradually decrease in intensity and frequency and often fade away. Negative thoughts (e.g., “I’m a bad person," or “Nobody likes me”) or ruminations about other people (“Will that girl like me?”) or about health issues (“Do I have AIDS?’) that can’t be quieted by reasonable evidence to the contrary, and that keep intruding on one’s awareness hour after hour, day after day despite all rational efforts to control, seem to diminish. Or, if they continue to occur, they are less distressing, and can be observed from more of a distance, with less worry or fear, and are less likely to trigger depression or other negative effects.

Which gets back to the longstanding debates between psychiatric lumpers and splitters. Do the benefits of NAC support the lumpers more than the splitters? Do they support the RDoC enthusiasts who are eagerly researching brain circuits? I think, in a way, such results do favor the lumpers. The improvement of irrational, difficult-to-control negative thoughts with NAC treatment in so many disorders makes it hard to avoid the conclusion that some common underlying circuitry is involved.

On the other hand, it’s not yet time for the splitters to go home conceding defeat. NAC doesn’t work for everyone, for one thing. But also, if the circuitry for ruminations is the same, why do some people with presumably hyperactive rumination circuits develop OCD and others develop bipolar disorder? And others yet, despite having severe ruminations, do not meet criteria for any psychiatric disorder? It’s possible that abnormal activity of particular brain circuits, starting early in life, may lead to the development of various different disorders over time, depending on your life experiences, coping patterns, etc. But how and why do their effects differ so much from one person to the next?

To me, the debates between the lumpers and the splitters are most useful when they help move science—and treatment—forward. In this case, with the emergence of NAC as a potentially beneficial treatment for a common symptom of many disorders, the goal posts are being moved usefully down the field.

Insel T, Cuthbert B, Garvey M, Heinssen R, Pine DS, Quinn K, Sanislow C, Wang P. Research domain criteria (RDoC): toward a new classification framework for research on mental disorders..

Caspi A, Moffitt TE. All for one and one for all: Mental disorders in one dimension. American Journal of Psychiatry. 2018 Apr 6175(9):831-44

Berk M, Malhi GS, Gray LJ, Dean OM. The promise of N-acetylcysteine in neuropsychiatry. Trends in pharmacological sciences. 2013 Mar 134(3):167-77


FREE A Level Biology Classification & Evolution Multiple Choice Questions

'If you keep trying the same old things, you'll keep getting the same old results'. Imaginative teaching ideas help stimulate students and improve student retention. I don't claim to be an expert but I hope that some of my ideas will help other teachers.

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This resource is a set of multiple choice questions to help students revise A Level Biology questions on classification & evolution

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'If you keep trying the same old things, you'll keep getting the same old results'. Imaginative teaching ideas help stimulate students and improve student retention. I don't claim to be an expert but I hope that some of my ideas will help other teachers.



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