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Amino Acids# - Biology

Amino Acids# - Biology


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Amino Acid Structure

Amino acids are the monomers that make up proteins. Each amino acid has the same core structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the alpha carbon known alternately as the R group, the variable group or the side-chain. For an additional introduction on amino acids, click here for a short (4 minute) video.

Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.

Attribution: Marc T. Facciotti (own work)

Note: Possible discussion

Recall that one of the learning goals for this class is that you (a) be able to recognize, in a molecular diagram, the backbone of an amino acid and its side chain (R-group) and (b) that you be able to draw a generic amino acid. Make sure that you practice both. You should be able to recreate something like the figure above from memory (a good use of your sketchbook is to practice drawing this structure until you can do it with the crutch of a book or the internet).

The Amino Acid Backbone

The name "amino acid" is derived from the fact that all amino acids contain both an amino group and carboxyl-acid-group in their backbone. There are 20 common amino acids present in natural proteins and each of these contain the same backbone. The backbone, when ignoring the hydrogen atoms, consists of the pattern:

N-C-C

When looking at a chain of amino acids it is always helpful to first orient yourself by finding this backbone pattern starting from the N terminus (the amino end of the first amino acid) to the C terminus (the carboxylic acid end of the last amino acid).

Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of the first amino acid is linked to the amino group of the second incoming amino acid. In the process, a molecule of water is released and a peptide bond is formed.
Try finding the backbone in the dipeptide formed from this reaction. The pattern you are looking for is: N-C-C-N-C-C

Attribution: Bis2A original image

The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration synthesis (condensation) reaction. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water and creating the peptide bond.

Amino Acid R group

The amino acid R group is a term that refers to the variable group on each amino acid. The amino acid backbone is identical on all amino acids, the R groups are different on all amino acids. For the structure of each amino acid refer to the figure below.

There are 20 common amino acids found in proteins, each with a different R group (variant group) that determines its chemical nature. R-groups are circled in teal. Charges are assigned assuming pH ~6.0. The full name, three letter abbreviation and single letter abbreviations are all shown.

Attribution: Marc T. Facciotti (own work)

Note: Possible Discussion

Let's think about the relevance of having 20 different amino acids. If you were using biology to build proteins from scratch, how might it be useful if you had 10 more different amino acids at your disposal? By the way, this is actually happening in a variety of research labs - why would this be potentially useful?

Each variable group on an amino acid gives that amino acid specific chemical properties (acidic, basic, polar, or nonpolar). You should be familiar with most of the functional groups in the R groups by now. The chemical properties associated with the whole collection of individual functional groups gives each amino acid R group unique chemical potential.

For example, amino acids such as valine, methionine, and alanine are typically nonpolar or hydrophobic in nature, while amino acids such as serine and threonine are said to have polar character and possess hydrophilic side chains.

Note: Practice

Using your knowledge of functional groups, try classifying each amino acid in the figure above as either having the tendency to be polar or nonpolar. Try to find other classification schemes and think make lists for yourself of the amino acids you would put into each group. You can also search the internet for amino acid classification schemes - you will notice that there are different ways of grouping these chemicals based on chemical properties. You may even find that there are contradictory schemes. Try to think about why this might be and apply your chemical logic to figuring out why certain classification schemes were adopted and why specific amino acids were placed in certain groups.

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Essential Amino Acids

Essential amino acids (EAAs) make up a group of nine amino acids that cannot be produced inside the body (de novo) but must be ingested as dietary protein. The building blocks of proteins, amino acids are bound together to produce polymer chain or folded proteins with a huge array of functions. There are three groups of amino acids: essential, non-essential, and conditional.


Amino Acids

Figure 1. Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group (Figure 1).

The name “amino acid” is derived from the fact that they contain both amino group and carboxyl-acid-group in their basic structure. As mentioned, there are 20 amino acids present in proteins. Ten of these are considered essential amino acids in humans because the human body cannot produce them and they are obtained from the diet.

For each amino acid, the R group (or side chain) is different (Figure 2).

Figure 2

Figure 2. There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature.

The chemical nature of the side chain determines the nature of the amino acid (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also known as basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the standard structure of an animo acid since its amino group is not separate from the side chain (Figure 2).

Amino acids are represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val. Just as some fatty acids are essential to a diet, some amino acids are necessary as well. They are known as essential amino acids, and in humans they include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary for construction of proteins in the body, although not produced by the body which amino acids are essential varies from organism to organism.

Figure 3. Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the amino group of the incoming amino acid. In the process, a molecule of water is released.

The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water. The resulting bond is the peptide bond (Figure 3).

The products formed by such linkages are called peptides. As more amino acids join to this growing chain, the resulting chain is known as a polypeptide. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require the addition of other chemical groups. Only after these modifications is the protein completely functional.

The Evolutionary Significance of Cytochrome c

Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally found in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the central ion of the heme gets alternately reduced and oxidized during electron transfer. Because this essential protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species in other words, evolutionary kinship can be assessed by measuring the similarities or differences among various species’ DNA or protein sequences.

Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that has been sequenced to date, 37 of these amino acids appear in the same position in all samples of cytochrome c. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, the single difference found was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.


Amino Acids# - Biology

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective they may serve in transport, storage, or membranes or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.

Figure 1. Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group (Figure 1).

The name “amino acid” is derived from the fact that they contain both amino group and carboxyl-acid-group in their basic structure. As mentioned, there are 20 amino acids present in proteins. Nine of these are considered essential amino acids in humans because the human body cannot produce them and they are obtained from the diet.

For each amino acid, the R group (or side chain) is different (Figure 2).

Practice Question

Figure 2. There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature.

Which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?

The chemical nature of the side chain determines the nature of the amino acid (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also known as basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the standard structure of an amino acid since its amino group is not separate from the side chain (Figure 2).

Amino acids are represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val. Just as some fatty acids are essential to a diet, some amino acids are necessary as well. They are known as essential amino acids, and in humans they include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary for construction of proteins in the body, although not produced by the body which amino acids are essential varies from organism to organism.

Figure 3. Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the amino group of the incoming amino acid. In the process, a molecule of water is released.

The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water. The resulting bond is the peptide bond (Figure 3).

The products formed by such linkages are called peptides. As more amino acids join to this growing chain, the resulting chain is known as a polypeptide. Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require the addition of other chemical groups. Only after these modifications is the protein completely functional.

The Evolutionary Significance of Cytochrome c

Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally found in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the central ion of the heme gets alternately reduced and oxidized during electron transfer. Because this essential protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species in other words, evolutionary kinship can be assessed by measuring the similarities or differences among various species’ DNA or protein sequences.

Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that has been sequenced to date, 37 of these amino acids appear in the same position in all samples of cytochrome c. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, the single difference found was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.


Amino Acids# - Biology

Amino acids are special organic molecules used by living organisms to make proteins. The main elements in amino acids are carbon, hydrogen, oxygen, and nitrogen. There are twenty different kinds of amino acids that combine to make proteins in our bodies. Our bodies can actually make some amino acids, but the rest we must get from our food.

Proteins are long chains of amino acids. There are thousands of different proteins in the human body. They provide all sorts of functions to help us survive.

Why are they important?

Proteins are essential for life. Around 20% of our body is made up of proteins. Every cell in our body uses proteins to perform functions.

Proteins are made inside cells. When a cell makes a protein it is called protein synthesis. The instructions for how to make a protein are held in DNA molecules inside the cell nucleus. The two major stages in making a protein are called transcription and translation.

The first step in making a protein is called transcription. This is when the cell makes a copy (or "transcript") of the DNA. The copy of DNA is called RNA because it uses a different type of nucleic acid called ribonucleic acid. The RNA is used in the next step, which is called translation.

The next step in making a protein is called translation. This is when the RNA is converted (or "translated") into a sequence of amino acids that makes up the protein.

  • The RNA moves to the ribosome. This type of RNA is called the "messenger" RNA. It is abbreviated as mRNA where the "m" is for messenger.
  • The mRNA attaches itself to the ribosome.
  • The ribosome figures out where to start on the mRNA by finding a special three letter "begin" sequence called a codon.
  • The ribosome then moves down the strand of mRNA. Every three letters represents another amino acid molecule. The ribosome builds a string of amino acids based on the codes in the mRNA.
  • When the ribosome sees the "stop" code, it ends the translation and the protein is complete.

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Fibrous Proteins

1. Collagen

  • Collagen is the most abundant protein of mammals that makes up about 25-33% of all the body proteins.
  • It is the principal structural element of the human body that is found in connective tissues such as tendons, cartilage, the organic matrix of bones, and the cornea of the eye.
  • Structurally, the collagen helix is a unique secondary structure quite distinct from the α helix. It is left-handed and has three amino acid residues per turn.
  • Collagen is also a coiled-coil, but with distinct tertiary and quaternary structures where three separate polypeptides, called α chains are supertwisted about each other.
  • Typically they contain about 35% glycine, 11% alanine, and 21% proline, and 4-hydroxyproline.

2. Keratin

  • Keratin or α-keratin is a fibrous protein that constitutes almost the entire dry weight of hair, wool, nails, claws, quills, horns, hooves, and much of the outer layer of skin in mammals.
  • The α-keratins are part of a broader family of proteins called intermediate filament (IF) proteins.
  • The α-keratin helix is a right-handed α-helix, the secondary structure found in many other proteins.
  • Two strands of α-keratin, oriented in parallel, are wrapped about each other to form a super twisted coil that amplifies the strength of the overall structure.
  • An individual polypeptide in the α -keratin coiled-coil has a relatively simple tertiary structure, dominated by an α -helical secondary structure with its helical axis twisted in a left-handed superhelix.
  • The intertwining of the two α -helical polypeptides in keratin acts as an example of a quaternary structure.

3. Elastin

  • Elastin is a major protein found in various organs that require elasticity like lungs, bladder, and elastic cartilage.
  • The polypeptide chain consists of tropoelastin protein, containing glycine and valine and modified alanine and proline residues.
  • It is classified as a fibrous protein due to its structural function and insolubility in water.
  • Elastin lacks a regular secondary structure and has cross-linkages of various protein sequences.
  • Elastin is also rich in glycine and proline, but it doesn’t have a glycine molecule like every third residue like in collagen.

Amino Acids

Amino acids are organic acids in which one or more hydrogen atoms attached to the hydrocarbon skeleton are replaced by equal number ofamino(-NH2) groups. Each amino acid contains at least one acidic carboxyl (-COOH) group and one basic amino (-NH2) group. Some amino acids may have an additional amino and/or a carboxyl group. All amino acids are made up of C2H2O and N2 while some of them contain Sulphur(S) in addition.

Types of Amino Acids

As constituent of proteins most of the natural amino acids are found. Several natural amino acids are now known that are not found in proteins but remain in free or bound form. So many types of amino acids are known to be present in protein. Those are:
1) Lysine
2) Valine
3) leucine
4) Isoleucine
5) Threonine
6) Methionine
7) phenyl alanine
8) Tryptophan
9) Glycine
10) Alanine
11) Serine
12) Aspartic acid
13) Glutamic acid
14) Arginine
15) Cysteine
16) Cystine
17) Tyrosine
18) Histidine
19) Proline
20) Hydroxyproline
21) Hydroxylysine
22) Aspargine
23) Glutamine.

Essential Amino Acids and Non-essential Amino Acids

From nutritional point of view, amongst the abovementioned amino acids, the first eight are called essential or indispensable amino acids as they are not synthesized in our body and their presence in diet is essential.
The remaining ones are referred to as non-essential or dispensable amino acids because they can be synthesized in the body and are not necessarily to be taken through diet. In addition to the eight essential amino acids, histidine and arginine are considered as semi-essential amino acids because these two amino acids are essential for infants but not for adults.

Classification of amino acids

Amino acids may also be classified into three groups according to the number of amino and carboxyl groups present in the molecule or according to the reaction in solution as follows: —

Neutral amino acids

Neutral amino acids have equal number of basic amino and acidic carboxyl groups. These may again be of two types—(a) mono amino mono carboxylic acid e.g., glycine, alanine, serine, valine etc., and (b) diamino dicarboxylic acid e.g., cystine.

Acidic amino acids

Mono-amino dicarboxylic acids are Acidic amino acids because they contain an extra acidic carboxylic group. Example: — aspartic acid and glutamic acid.

Basic amino acids

Basic amino acids are diamino monocarboxylic acids e.g., lysine, hydroxylysine and arginine.

According to their metabolic fates, amino acids are of three types, those are: —

Glycogenic amino acids

Amino acids which can enter into the neoglucogenic pathway to produce glucose and glycogen are called glyogenic aminoacids. They comprise glycine, alanine, serine, cysteine, valine, methionine, glutamine, aspartic acid, histidine, arginine, proline and hydroxy proline.

Ketogenic amino acids

Amino acids whose carbon skeletons are converted to ketone bodies and not to glucose are called ketogenic amino acids. They comprise leucine and lysine.

Glycogenic-ketogenic amino acids

Amino acids whose carbon skeletons are converted partly to glucose and partly to ketone bodies belong to this group. They include phenyl alanine, tyrosine, tryptophan, isoleucine and threonine.
And the amino acids contain sulphur: -

Sulphur containing amino acids

There are three amino acids namely methionine, cysteine and cystine belong to this group because their molecules contain sulphur (S).


The basic hierarchy of protein structure

Two amino acids can join together by releasing a water molecule in the process through a bond called the peptide bond. Therefore, many amino acids join together to form a protein. There are a certain structural hierarchy of proteins.

The linear sequence of amino acids forming a long chain is referred to as the primary structure of a protein. This is the simplest form. Now, these peptide bonds can rotate about its axis which gives rise to something called the torsional angles. The Cα-C forms the psi angle and Cα-N forms the phi angle. If a stretch of the polypeptide has the same phi and psi angle repeatedly, that particular stretch would locally fold into a specific structure. This localized folding is referred to as the secondary structure of a protein. Therefore, a single protein can have a lot of secondary structures. Some examples of secondary structures are alpha-helix, beta sheets and beta turns. When the secondary structure containing proteins fold in a 3-dimensional form, it is called the tertiary structure and if a protein contains different tertiary structured chains, it is referred to as the quaternary structure

This tertiary and Quaternary structure of a protein is absolutely essential for its particular function. If these structures are disrupted, the function of the protein disrupts as well.


Amino Acids# - Biology

The Forum for Amino Acid, Peptide and Protein Research

Amino Acids publishes contributions from all fields of amino acid and protein research: analysis, separation (proteomics), synthesis, biosynthesis, evolution, folding, structure, stability, dynamics, medicinal chemistry, catabolism, cross linking amino acids, racemization/enantiomers, modification of amino acids such as phosphorylation, methylation, acetylation, hydroxylation and glycosylation. The journal also welcomes papers on new roles for amino acids and proteins in physiology and pathophysiology, biology, amino acid analogues, polyamines, labeled amino acids, peptides, stable and radioactive isotopes of amino acids, excitatory amino acids, unusual amino acids, and peptides. Applications include medicine (gastroenterology, nephrology, psychiatry, neurology, oncology), biochemistry, structural biology, agriculture and plants, food chemistry, nutrition, microbiology, neurochemistry, pharmacology, and sports. We also encourage the submissions of computational papers and interdisciplinary research such as economic, social sciences and humanities.

  • Covers all aspects of amino acid and protein research
  • Explores analysis, separation, synthesis, biosynthesis, cross linking amino acids, racemization/enantiomers, modification of amino acids such as phosphorylation
  • Includes biochemistry, food chemistry, nutrition, neurology, psychiatry, pharmacology, nephrology, gastroenterology, microbiology
  • 91% of authors who answered a survey reported that they would definitely publish or probably publish in the journal again