Information

2.5.4: Amino Acids - Biology


An amino acid contains an amino group, a carboxyl group, and an R group, and it combines with other amino acids to form polypeptide chains.

Learning Objectives

  • Describe the structure of an amino acid and the features that confer its specific properties

Key Points

  • Each amino acid contains a central C atom, an amino group (NH2), a carboxyl group (COOH), and a specific R group.
  • The R group determines the characteristics (size, polarity, and pH) for each type of amino acid.
  • Peptide bonds form between the carboxyl group of one amino acid and the amino group of another through dehydration synthesis.
  • A chain of amino acids is a polypeptide.

Key Terms

  • amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
  • R group: The R group is a side chain specific to each amino acid that confers particular chemical properties to that amino acid.
  • polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds.

Structure of an Amino Acid

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. In the aqueous environment of the cell, the both the amino group and the carboxyl group are ionized under physiological conditions, and so have the structures -NH3+ and -COO, respectively. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. This R group, or side chain, gives each amino acid proteins specific characteristics, including size, polarity, and pH.

Types of Amino Acids

The name “amino acid” is derived from the amino group and carboxyl-acid-group in their basic structure. There are 21 amino acids present in proteins, each with a specific R group or side chain. Ten of these are considered essential amino acids in humans because the human body cannot produce them and they must be obtained from the diet. All organisms have different essential amino acids based on their physiology.

Characteristics of Amino Acids

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 composition of the side chain determines the characteristics of the amino acid. Amino acids such as valine, methionine, and alanine are nonpolar (hydrophobic), while amino acids such as serine, threonine, and cysteine are polar (hydrophilic). The side chains of lysine and arginine are positively charged so these amino acids are also known as basic (high pH) amino acids. Proline is an exception to the standard structure of an amino acid because its R group is linked to the amino group, forming a ring-like structure.

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.

Peptide Bonds

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. When two amino acids are covalently attached by a peptide bond, the carboxyl group of one amino acid and the amino group of the incoming amino acid combine and release a molecule of water. Any reaction that combines two monomers in a reaction that generates H2O as one of the products is known as a dehydration reaction, so peptide bond formation is an example of a dehydration reaction.

Polypeptide Chains

The resulting chain of amino acids is called a polypeptide chain. 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. When reading or reporting the amino acid sequence of a protein or polypeptide, the convention is to use the N-to-C direction. That is, the first amino acid in the sequence is assumed to the be one at the N terminal and the last amino acid is assumed to be the one at the C terminal.

Although the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically any polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have folded properly, combined with any additional components needed for proper functioning, and is now functional.


Amino Acid Codon Table

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Table of codons


Genetic Code and Amino Acid Translation

Table 1 shows the genetic code of the messenger ribonucleic acid (mRNA), i.e. it shows all 64 possible combinations of codons composed of three nucleotide bases (tri-nucleotide units) that specify amino acids during protein assembling.

Each codon of the deoxyribonucleic acid (DNA) codes for or specifies a single amino acid and each nucleotide unit consists of a phosphate, deoxyribose sugar and one of the 4 nitrogenous nucleotide bases, adenine (A), guanine (G), cytosine (C) and thymine (T). The bases are paired and joined together by hydrogen bonds in the double helix of the DNA. mRNA corresponds to DNA (i.e. the sequence of nucleotides is the same in both chains) except that in RNA, thymine (T) is replaced by uracil (U), and the deoxyribose is substituted by ribose.

The process of translation of genetic information into the assembling of a protein requires first mRNA, which is read 5' to 3' (exactly as DNA), and then transfer ribonucleic acid (tRNA), which is read 3' to 5'. tRNA is the taxi that translates the information on the ribosome into an amino acid chain or polypeptide.

For mRNA there are 4 3 = 64 different nucleotide combinations possible with a triplet codon of three nucleotides. All 64 possible combinations are shown in Table 1. However, not all 64 codons of the genetic code specify a single amino acid during translation. The reason is that in humans only 20 amino acids (except selenocysteine) are involved in translation. Therefore, one amino acid can be encoded by more than one mRNA codon-triplet. Arginine and leucine are encoded by 6 triplets, isoleucine by 3, methionine and tryptophan by 1, and all other amino acids by 4 or 2 codons. The redundant codons are typically different at the 3rd base. Table 2 shows the inverse codon assignment, i.e. which codon specifies which of the 20 standard amino acids involved in translation.

Table 1. Genetic code: mRNA codon -> amino acid

1st
Base
2nd
Base
3rd
Base
U C A G
U Phenylalanine Serine Tyrosine Cysteine U
Phenylalanine Serine Tyrosine Cysteine C
Leucine Serine Stop Stop A
Leucine Serine Stop Tryptophan G
C Leucine Proline Histidine Arginine U
Leucine Proline Histidine Arginine C
Leucine Proline Glutamine Arginine A
Leucine Proline Glutamine Arginine G
A Isoleucine Threonine Asparagine Serine U
Isoleucine Threonine Asparagine Serine C
Isoleucine Threonine Lysine Arginine A
Methionine (Start) 1 Threonine Lysine Arginine G
G Valine Alanine Aspartate Glycine U
Valine Alanine Aspartate Glycine C
Valine Alanine Glutamate Glycine A
Valine Alanine Glutamate Glycine G

Table 2. Reverse codon table: amino acid -> mRNA codon

Amino acid mRNA codons Amino acid mRNA codons
Ala/A GCU, GCC, GCA, GCG Leu/L UUA, UUG, CUU, CUC, CUA, CUG
Arg/R CGU, CGC, CGA, CGG, AGA, AGG Lys/K AAA, AAG
Asn/N AAU, AAC Met/M AUG
Asp/D GAU, GAC Phe/F UUU, UUC
Cys/C UGU, UGC Pro/P CCU, CCC, CCA, CCG
Gln/Q CAA, CAG Ser/S UCU, UCC, UCA, UCG, AGU, AGC
Glu/E GAA, GAG Thr/T ACU, ACC, ACA, ACG
Gly/G GGU, GGC, GGA, GGG Trp/W UGG
His/H CAU, CAC Tyr/Y UAU, UAC
Ile/I AUU, AUC, AUA Val/V GUU, GUC, GUA, GUG
START AUG STOP UAG, UGA, UAA

The direction of reading mRNA is 5' to 3'. tRNA (reading 3' to 5') has anticodons complementary to the codons in mRNA and can be "charged" covalently with amino acids at their 3' terminal. According to Crick the binding of the base-pairs between the mRNA codon and the tRNA anticodon takes place only at the 1st and 2nd base. The binding at the 3rd base (i.e. at the 5' end of the tRNA anticodon) is weaker and can result in different pairs. For the binding between codon and anticodon to come true the bases must wobble out of their positions at the ribosome. Therefore, base-pairs are sometimes called wobble-pairs.

Table 3 shows the possible wobble-pairs at the 1st, 2nd and 3rd base. The possible pair combinations at the 1st and 2nd base are identical. At the 3rd base (i.e. at the 3' end of mRNA and 5' end of tRNA) the possible pair combinations are less unambiguous, which leads to the redundancy in mRNA. The deamination (removal of the amino group NH2) of adenosine (not to confuse with adenine) produces the nucleotide inosine (I) on tRNA, which generates non-standard wobble-pairs with U, C or A (but not with G) on mRNA. Inosine may occur at the 3rd base of tRNA.

Table 3. Base-pairs: mRNA codon -> tRNA anticodon

Table 3 is read in the following way: for the 1st and 2nd base-pairs the wobble-pairs provide uniqueness in the way that U on tRNA always emerges from A on mRNA, A on tRNA always emerges from U on mRNA, etc. For the 3rd base-pair the genetic code is redundant in the way that U on tRNA can emerge from A or G on mRNA, G on tRNA can emerge from U or C on mRNA and I on tRNA can emerge from U, C or A on mRNA. Only A and C at the 3rd place on tRNA are unambiguously assigned to U and G at the 3rd place on mRNA, respectively.

Due to this combination structure a tRNA can bind to different mRNA codons where synonymous or redundant mRNA codons differ at the 3rd base (i.e. at the 5' end of tRNA and the 3' end of mRNA). By this logic the minimum number of tRNA anticodons necessary to encode all amino acids reduces to 31 (excluding the 2 STOP codons AUU and ACU, see Table 5). This means that any tRNA anticodon can be encoded by one or more different mRNA codons (Table 4). However, there are more than 31 tRNA anticodons possible for the translation of all 64 mRNA codons. For example, serine has a fourfold degenerate site at the 3rd position (UCU, UCC, UCA, UCG), which can be translated by AGI (for UCU, UCC and UCA) and AGC on tRNA (for UCG) but also by AGG and AGU. This means, in turn, that any mRNA codon can also be translated by one or more tRNA anticodons (see Table 5).

The reason for the occurrence of different wobble-pairs encoding the same amino acid may be due to a compromise between velocity and safety in protein synthesis. The redundancy of mRNA codons exist to prevent mistakes in transcription caused by mutations or variations at the 3rd position but also at other positions. For example, the first position of the leucine codons (UCA, UCC, CCU, CCC, CCA, CCG) is a twofold degenerate site, while the second position is unambiguous (not redundant). Another example is serine with mRNA codons UCA, UCG, UCC, UCU, AGU, AGC. Of course, serine is also twofold degenerate at the first position and fourfold degenerate at the third position, but it is twofold degenerate at the second position in addition. Table 4 shows the assignment of mRNA codons to any possible tRNA anticodon in eukaryotes for the 20 standard amino acids involved in translation. It is the reverse codon assignment.

Table 4. Reverse amino acid encoding: amino acid -> tRNA anticodon -> mRNA codon

While it is not possible to predict a specific DNA codon from an amino acid, DNA codons can be decoded unambiguously into amino acids. The reason is that there are 61 different DNA (and mRNA) codons specifying only 20 amino acids. Note that there are 3 additional codons for chain termination, i.e. there are 64 DNA (and thus 64 different mRNA) codons, but only 61 of them specify amino acids.

Table 5 shows the genetic code for the translation of all 64 DNA codons, starting from DNA over mRNA and tRNA to amino acid. In the last column, the table shows the different tRNA anticodons minimally necessary to translate all DNA codons into amino acids and sums up the number in the final row. It reveals that the minimum number of tRNA anticodons to translate all DNA codons is 31 (plus 2 STOP codons). The maximum number of tRNA anticodons that can emerge in amino acid transcription is 70 (plus 3 STOP codons).

Table 5. Genetic code: DNA -> mRNA codon -> tRNA anticodon -> amino acid

Note:
1 The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's coding region is where translation into protein begins.


5 Answers 5

Although the question shows considerable effort to achieve clarity, the way it is phrased as:

How many molecules of nucleoside triphosphate… [does] it take to release enough energy

still allows ambiguity, as I would not really regard the NTPs involved in protein synthesis “releasing energy”. So let us consider two reformulations of the question, as the explanation of the answers is of more scientific interest than the actual answers.

1. How many molecules of NTP are hydrolysed in the reactions causing the formation of one peptide bond on the ribosome?

Formation of each peptide bond involves a cycle consisting of the introduction of a single new aminoacyl-tRNA to the A site of a ribosome carrying a growing polypeptide chain (or initiator tRNA for the first peptide bond), the peptidyl transferase reaction, and than translocation of the extended peptidyl-tRNA from A- to P-site. (See, e.g. Berg et al. online — Ch. 29)

1 ATP is hydrolysed in the aminoacylation reaction:

1 GTP is hydrolysed in the aatRNA binding reaction catalysed by EF-Tu/EF1.

1 GTP is hydrolysed in the translocation reaction catalysed by EF-G/EF2

No NTP is consumed directly in the peptidyl transferase reaction — the energy for bond formation comes from the ‘activated’ aminoacyl-tRNA.

2. What is the total energetic cost in molecules of ATP for the formation of one peptide bond?

Here one might argue that:

The additional ATP occurs if one considers the total energetic cost of the aminoacylation reaction as 2 ATP, not 1 ATP. This arises from the fact that the ATP is hydrolysed to AMP (+PPi) and not ADP. Recycling of the AMP involves first the use of 1 molecule of ATP in the adenylate kinase reaction to produce ADP:

followed by the energy (from membrane ATP synthase) to regenerate ATP from ADP:


Visualising molecules

Identification of biochemicals.

Using online flashcards and a database, students learn how to identify biological molecules and to distinguish between them. Examples included are monosaccharides such as alpha-D-glucose, beta-D-glucose and D-ribose, a disaccharide and lipids such as a saturated fatty acid, a triglyceride, and a phospholipid. There is also a polypeptide, two amino acids linked by a peptide bond and a generalized amino acid.

Lesson Description

Guiding Questions

Can you recognise the structures of some important biological molecules, like glucose and fructose?

How might the size and shape of the molecules change their properties?

How is a starch molecule different to a hundred glucose molecules?

Activity 1 - Key points about biological molecules

Using these online flashcards practise some of the details about the structure of these biological macromolecules. (click the eye to show the flashcards)

Activity 2 - Visualising molecules

Answer the questions below using the 3D visualisations of biological molecules. Pause the video to see the molecule or click the link to the Jmol database and manipulate the molecules directly on Chemspider.
There is also a Visualising molecules student worksheet.

In the images carbon is coloured grey, oxygen is red and hydrogen white. In proteins nitrogen is blue.

Monosaccharides

  1. What is the difference between alpha and beta glucose?
  2. How does D-ribose differ from the two glucose molecules.

Alpha-D-glucose


http://www.chemspider.com/Chemical-Structure.71358.html

Beta-D-glucose


http://www.chemspider.com/Chemical-Structure.58238.html

D-ribose


http://www.chemspider.com/Chemical-Structure.5575.html

Disaccharides

  1. What is the characteristic feature of these three disaccharides?
  2. How many carbon atoms do each of the monosaccharide components of the disaccharides have?

Maltose

http://www.chemspider.com/Chemical-Structure.388329.html

Sucrose


http://www.chemspider.com/Chemical-Structure.5768.html

Lactose


http://www.chemspider.com/Chemical-Structure.389820.html

Lipids

  1. What are the two main differences between a phospholipid and a triglyceride?
  2. How does a saturated fatty acid attach to glycerol in a triglyceride?
  3. Which of these molecules most resembles cholesterol? Why?

Saturated fatty acid


http://www.chemspider.com/Chemical-Structure.2863.html

Triglyceride diagram

Phospholipid diagram

Glycerol


http://www.chemspider.com/Chemical-Structure.733.html

A Steroid - Cholesterol


http://www.chemspider.com/Chemical-Structure.5775.html

Another Triglyceride


http://www.chemspider.com/Chemical-Structure.10394.html

Proteins

  1. Describe the two ends of the amino acid Glycine - this is the simplest amino acid as the R-group is just Hydrogen.
  2. Which two atoms bond together to form a peptide bond between two amino acids?
  3. How can you spot a peptide bond in larger molecules?
  4. In a polypeptide what are the molecular groups at each end of the chain?

Glycine - a simple amino acid


http://www.chemspider.com/Chemical-Structure.730.html

Two Amino acids (linked by a peptide bond)


http://www.chemspider.com/Chemical-Structure.88624.html

Polypeptide (with 4 amino acids)


http://www.chemspider.com/Chemical-Structure.16607924.html

Further details about the structures of some of these molecules can be found by clicking the links to Chemspider by each video above. Chemspider is a free chemical structure database providing structures and chemical properties of over 32 million structures.

Student worksheet of questions

Answer the following questions as you make notes: Visualising molecules worksheet

Activity 3 IB Style Questions

Test your knowledge with these IB style questions about biological molecules which you have just studied.

Teachers notes

NoS TOK - Opportunity

This activity could be used to illustrate some points about NOS and TOK and engage the students in a really interesting analysis of the usefulness in Biology of 2D diagrams of 3D chemicals.

Some scientists draw Ribose with the -OH and -H groups in different positions in a 2D diagram.
Are they wrong? How is it possible that there can be disagreement?

Take a look at this image of Ribose it has the -OH group on C1 carbon going upwards. In IB past paper question in May 2004 and 2008 there were molecules of ribose with the C1 -OH going down. I couldn't find a diagram the other way round.

Which diagram is wrong? Could they both be right?

The problem comes from trying to represent a 3D molecule in a simplified 2D diagram.
In fact the four bonds on a Carbon atom (in methane) form a tetrahedral shape. The diagrams we learned to draw last lesson are simplifications. I would argue that they are useful 2D models because they help biology students to understand the nature of biological molecules and from that understanding the functioning of enzymes and the properties of cell membranes and other cell organelles. All of this without worrying about 3D shape and bond angles - which IB chemists have to do.

In RIbose if the -O- is at the top and C1 on the right then the C1 -OH group comes forwards. See this video clip.

If you view from slightly above then -OH looks lower than H on the C1. If you look from below then the -OH looks higher.
The best way to see is using the 3D rendering of the Chemspider 3D JS model seen in this lesson.

I think this is a really interesting point for discussion with students. It would cover the NOS points on the use of models (1.10) and it would address the TOK dilemma between simplification to aid understanding and the the accuracy of complex models.

This problem of experts disagreeing features in TOK Essay titles:

Title 5 (2007):
Given access to the same facts, how is it possible that there can be disagreement between experts in a discipline?

In fact, like many monosaccharides, ribose exists in an equilibrium among 5 forms:

  1. the linear form
  2. alpha-ribofuranose
  3. beta-ribofuranose
  4. alpha-ribopyranose
  5. beta-ribopyranose.

The beta-ribopyranose form predominates in aqueous solution (59%).
The ribose form &beta-D-ribofuranose(13%) forms part of the backbone of RNA.

The aim of this lesson is to "flip the classroom" so that students make the best use of valuable lab time to complete the experiment while covering the factual theory work as homework, preferably before the lesson.

The IB-style questions can be used to check that the students have understood the simple facts and molecular names.

The Jmol 3D visualisations of molecules is a great introduction to Jmol and the possibilities of this sort of ICT. This is a simple biological gallery of Jmol 3D molecule visualisations.

The model answers are on separate pages so that teachers can control student access to these pags.


Watch the video: 5 2 Η ροή της γενετικής πληροφορίας DNA,RNA (January 2022).