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9.3: Exercise 1 - The 1-letter code for amino acids - Biology

9.3: Exercise 1 - The 1-letter code for amino acids - Biology


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You may find NCBI’s Amino Acid Explorer helpful for this exercise. You can access Amino Acid Explorer through Google or directly at:

www.ncbi.nlm.nih.gov/Class/St...a_explorer.cgi


1. Under the amino sequence below, write the same sequence using the 1-letter code. Met-Glu-Asn-Asp-Glu-Leu-Pro-Ile-Cys-Lys-Glu-Asp-Pro-Glu-Cys-Lys-Glu-Asp

2. What is the net charge of this peptide? (Assign -1 for each acidic amino acid and +1 for each basic amino acid. Add up the total charges.)

3. Using the Venn diagram above, propose a conservative substitution for:
Trp - His - ​​​​​​​Arg - ​​​​​​​​​​​​​​Leu -

4. Write the name of a music group that you enjoy. Then transpose the name into an amino acid sequence written with the 3-letter code. Pass the amino acid sequence to a friend and have him/her decode it. (Note: the 1-letter code uses all of the alphabet, except B, J, O, U, X and Z).


Amino acids

Amino acids are the building blocks of proteins - they create the proteins primary structure. There are 20 naturally occurring amino acids. Amino acids exist in proteins as L-optical isomers, however, they can exist as D-isomers in isolated examples, e.g. some bacterial cell walls contain D-isomers. When two amino acids join they form a peptide bond. This bond works as a partial double bond causing the amino acids to have cis/trans isomers. Although most commonly found in trans. All amino acids are amphoteric meaning they can act as both a base and an acid due to their amino and carboyxl groups respectively [1] .

Amino Acids are the monomers that make up proteins by joining in condensation reactions to form peptide bonds between themselves. When an Amino Acid is part of a protein it is known as an Amino Acid residue, it has the same side chain but it's alpha Amino and carboxyl groups are now part of peptide bonds. All amino acids have an alpha carboxylic acid group, an alpha amine group and a hydrogen atom bonded to a central carbon along with a fourth variable group. This group varies in the 20 essential amino acids and generally allows amino acids to exhibit sterioisomerism to create optical isomers D and L. The only exception to this being the simplest amino acid glycine with its variable group being another hydrogen atom. This prevents sterioisomerism as there aren't four different groups then bonded to the central carbon - there is no chiral centre [2] . 

Amino acids can also be characterised as polar or non-polar and these dictate the amino acid function. There are 10 non-polar amino acids found in protein core, and there are 10 polar amino acids. These have enzymatic roles and can be used to bind DNA, metals and other naturally occurring ligands. There are essential amino acids and non-essential amino acids. Essential amino acids are the ones that the body cannot synthesise on its own. The essential amino acids in humans are: histidine, leucine, isoleucine, lysine, methionine, valine, phenylalanine, tyrosine and tryptophan [3] . These amino acids have to be supplied to the body via digested proteins that are then absorbed in the intestine and transported in the blood to where they are needed [4] . The digestion of cellular proteins is also an important source for amino acids. Non-essential amino acids can be synthesised from compounds already existing in the body such as how serine is synthesised from glycine [5] .

Amino acids have been abbreviated into a 3 letter code as well as a 1 letter code. For example, glycine has the 3 letter code 'Gly' and is assigned the letter 'G' (see single letter amino acid codes).

The table below lists the 20 Amino acids, their single letter code, three letter code, their charges, and side chain polarity:


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.


Amino acid

Amino acids are organic compounds that contain amino (–NH2) and carboxyl (–COOH) functional groups, along with a side chain (R group) specific to each amino acid. [1] The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known as of 1983 (though only 20 appear in the genetic code) and can be classified in many ways. [2] They can be classified according to the core structural functional groups' locations as alpha- (α-) , beta- (β-) , gamma- (γ-) or delta- (δ-) amino acids other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. [3] Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.

In biochemistry, amino acids which have the amine group attached to the (alpha-) carbon atom next to the carboxyl group have particular importance. They are known as 2-, alpha-, or α-amino acids (generic formula H2NCHRCOOH in most cases, [a] where R is an organic substituent known as a "side chain") [4] often the term "amino acid" is used to refer specifically to these. They include the 22 proteinogenic ("protein-building") amino acids, [5] [6] [7] which combine into peptide chains ("polypeptides") to form the building blocks of a vast array of proteins. [8] These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics. [9]

Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids. The other two ("nonstandard" or "non-canonical") are selenocysteine (present in many prokaryotes as well as most eukaryotes, but not coded directly by DNA), and pyrrolysine (found only in some archaea and one bacterium). Pyrrolysine and selenocysteine are encoded via variant codons for example, selenocysteine is encoded by stop codon and SECIS element. [10] [11] [12] N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts) is generally considered as a form of methionine rather than as a separate proteinogenic amino acid. Codon–tRNA combinations not found in nature can also be used to "expand" the genetic code and form novel proteins known as alloproteins incorporating non-proteinogenic amino acids. [13] [14] [15]

Many important proteinogenic and non-proteinogenic amino acids have biological functions. For example, in the human brain, glutamate (standard glutamic acid) and gamma-aminobutyric acid ("GABA", nonstandard gamma-amino acid) are, respectively, the main excitatory and inhibitory neurotransmitters. [16] Hydroxyproline, a major component of the connective tissue collagen, is synthesised from proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells. Carnitine is used in lipid transport. Nine proteinogenic amino acids are called "essential" for humans because they cannot be produced from other compounds by the human body and so must be taken in as food. Others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also vary from species to species. [b] Because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, feed, and food technology. Industrial uses include the production of drugs, biodegradable plastics, and chiral catalysts.

History

The first few amino acids were discovered in the early 19th century. [17] [18] In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, the first amino acid to be discovered. [19] [20] Cystine was discovered in 1810, [21] although its monomer, cysteine, remained undiscovered until 1884. [20] [22] Glycine and leucine were discovered in 1820. [23] The last of the 20 common amino acids to be discovered was threonine in 1935 by William Cumming Rose, who also determined the essential amino acids and established the minimum daily requirements of all amino acids for optimal growth. [24] [25]

The unity of the chemical category was recognized by Wurtz in 1865, but he gave no particular name to it. [26] The first use of the term "amino acid" in the English language dates from 1898, [27] while the German term, Aminosäure, was used earlier. [28] Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one amino acid with the carboxyl group of another, resulting in a linear structure that Fischer termed "peptide". [29]

General structure

In the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the carboxyl group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids. [30] These include amino acids such as proline which contain secondary amines, which used to be often referred to as "imino acids". [31] [32] [33]

Isomerism

Alpha-amino acids are the common natural forms of amino acids. With the exception of glycine, other natural amino acids adopt the L configuration. [34] While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome.

The L and D convention for amino acid configuration refers not to the optical activity of the amino acid itself but rather to the optical activity of the isomer of glyceraldehyde from which that amino acid can, in theory, be synthesized (D-glyceraldehyde is dextrorotatory L-glyceraldehyde is levorotatory). In alternative fashion, the (S) and (R) designators are used to indicate the absolute configuration. Almost all of the amino acids in proteins are (S) at the α carbon, with cysteine being (R) and glycine non-chiral. [35] Cysteine has its side chain in the same geometric location as the other amino acids, but the R/S terminology is reversed because sulfur has higher atomic number compared to the carboxyl oxygen which gives the side chain a higher priority by the Cahn-Ingold-Prelog sequence rules, whereas the atoms in most other side chains give them lower priority compared to the carboxyl group. [ citation needed ]

D-amino acid residues are found in some proteins, but they are rare.

Side chains

Amino acids are designated as α- when the nitrogen atom is attached to the carbon atom adjacent to the carboxyl group: in this case the compound contains the substructure N–C–CO2. Amino acids with the sub-structure N–C–C–CO2 are classified as β- amino acids. γ-Amino acids contain the substructure N–C–C–C–CO2, and so on. [36]

Amino acids are usually classified by the properties of their side chain into four groups. The side chain can make an amino acid a weak acid or a weak base, and a hydrophile if the side chain is polar or a hydrophobe if it is nonpolar. [34] The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side chains that are linear these are leucine, isoleucine, and valine. Proline is the only proteinogenic amino acid whose side-group links to the α-amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position. [34] In chemical terms, proline is, therefore, an imino acid, since it lacks a primary amino group, [37] although it is still classed as an amino acid in the current biochemical nomenclature [38] and may also be called an "N-alkylated alpha-amino acid". [39]

Zwitterions

In aqueous solution amino acids exist in two forms (as illustrated at the right), the molecular form and the zwitterion form in equilibrium with each other. The two forms coexist over the pH range pK1 − 2 to pK2 + 2 , which for glycine is pH 0–12. The ratio of the concentrations of the two isomers is independent of pH. The value of this ratio cannot be determined experimentally.

Because all amino acids contain amine and carboxylic acid functional groups, they are amphiprotic. [34] At pH = pK1 (approximately 2.2) there will be equal concentration of the species NH +
3 CH(R)CO
2 H and NH +
3 CH(R)CO −
2 and at pH = pK2 (approximately 10) there will be equal concentration of the species NH +
3 CH(R)CO −
2 and NH
2 CH(R)CO −
2 . It follows that the neutral molecule and the zwitterion are effectively the only species present at biological pH. [40]

It is generally assumed that the concentration of the zwitterion is much greater than the concentration of the neutral molecule on the basis of comparisons with the known pK values of amines and carboxylic acids.


Exercises¶

Exercise 1: Find pairs of characters¶

Write a function count_pairs(dna, pair) that returns the number of occurrences of a pair of characters ( pair ) in a DNA string ( dna ). For example, calling the function with dna as 'ACTGCTATCCATT' and pair as 'AT' will return 2. Filename: count_pairs.py .

Exercise 2: Count substrings¶

This is an extension of Exercise 1: Find pairs of characters: count how many times a certain string appears in another string. For example, the function returns 3 when called with the DNA string 'ACGTTACGGAACG' and the substring 'ACG' .

Hint. For each match of the first character of the substring in the main string, check if the next n characters in the main string matches the substring, where n is the length of the substring. Use slices like s[3:9] to pick out a substring of s .

Exercise 3: Allow different types for a function argument¶

Consider the family of find_consensus_v* functions from the section Analyzing the Frequency Matrix. The different versions work on different representations of the frequency matrix. Make a unified find_consensus function that accepts different data structures for the frequency_matrix . Test on the type of data structure and perform the necessary actions. Filename: find_consensus.py .

Exercise 4: Make a function more robust¶

Consider the function get_base_counts(dna) from the section Finding Base Frequencies, which counts how many times A , C , G , and T appears in the string dna :

Unfortunately, this function crashes if other letters appear in dna . Write an enhanced function get_base_counts2 which solves this problem. Test it on a string like 'ADLSTTLLD' . Filename: get_base_counts2.py .

Exercise 5: Find proportion of bases inside/outside exons¶

Consider the lactase gene as described in the sections Translating Genes into Proteins and Some Humans Can Drink Milk, While Others Cannot. What is the proportion of base A inside and outside exons of the lactase gene?

Hint. Write a function get_exons , which returns all the substrings of the exon regions concatenated. Also write a function get_introns , which returns all the substrings between the exon regions concatenated. The function get_base_frequencies from the section Finding Base Frequencies can then be used to analyze the frequencies of bases A, C, G, and T in the two strings.

Exercise 6: Speed up Markov chain mutation¶

The functions transition and mutate_via_markov_chain from the section Random Mutations of Genes were made for being easy to read and understand. Upon closer inspection, we realize that the transition function constructs the interval_limits every time a random transition is to be computed, and we want to run a large number of transitions. By merging the two functions, pre-computing interval limits for each from_base , and adding a loop over N mutations, one can reduce the computation of interval limits to a minimum. Perform such an efficiency enhancement. Measure the CPU time of this new function versus the mutate_via_markov_chain function for 1 million mutations. Filename: markov_chain_mutation2.py .

Exercise 7: Extend the constructor in class Gene¶

Modify the constructor in class Gene from the section Classes for DNA Analysis such that giving no arguments to the constructor makes the class call up the generate_string method (from the dna_functions module) which generates a random DNA sequence. Filename: dna_classes2.py .


9.3: Exercise 1 - The 1-letter code for amino acids - Biology

This module provides an extensive description of the structures of biological macromolecules and their interactions. It aims to show how the basis of their reactivity can be understood in terms of chemical laws and concepts.

On completion of the module a student should be able to

a) mechanistically depict the typical reactivity of amino acids, nucleotides and simple carbohydrates

b) depict the primary, secondary, tertiary and quaternary structures of proteins, polysaccharides, nucleic acids and phospholipid bilayers, discuss their size and describe how their biological functions relate to their chemical structure and reactivity

c) explain the different types of non-covalent interactions at the molecular level and be able to translate the concepts of hydrogen-bonding, van der Waals interactions, hydrophobic interactions, hydrophilic interactions and salt bridges into a description of macromolecular structure and how small ligands interact with enzymes

d) give an overview of how enzymes function within biological systems, and write mechanisms for specific examples of hydrolytic and redox enzymes

e) explain the Michaelis-Menten model of enzyme kinetics and be able to quantitatively describe enzyme catalysed reactions using the Michaelis-Menten equation

f) explain the chemistry of DNA replication, mutagenesis and repair processes

g) depict the chemistry underlying transcription and translation, and explain how this can be used to manufacture a protein with a given amino acid sequence

h) draw mechanisms for Edman degradation of proteins and the reaction with cyanogen bromide.

How the module will be delivered

17 x 1 h lectures, 3 x 1h workshops, 7 h practical

Skills that will be practised and developed

On completion of the module the student will be able to:

a) rationalise biological reaction mechanisms using the curly arrow formalism of organic chemistry

b) suggest biological functions and biologically relevant reactivity of previously unseen molecules.

Discipline Specific (including practical) Skills:

On completion of the module the student will have a greater awareness of how to apply the principles of chemical reactivity to more complex biological systems. The student will be able to use on-line databases to search for function and structure of biological macromolecules.

How the module will be assessed

A written exam (2 h) will test the student&rsquos knowledge and understanding as elaborated under the learning outcomes. The coursework (workshops and tutorials) will allow the student to demonstrate his/her ability to judge and critically review relevant information. Practical skills will be assessed via a laboratory-based exercise.

Assessment Breakdown

Type % Title Duration(hrs)
Online Examination - Spring Semester 70 Chemical Biology Ii: Introduction To Enzyme And Nucleic Acid 2
Written Assessment 15 Workshops N/A
Practical-Based Assessment 15 Practical Work N/A

Syllabus content

Biomacromolecules and their building blocks &ndash amino acids, carbohydrates and nucleotides.

Amino acid side chain functional groups - classification into hydrophobic, hydrophilic, charged, aromatic.

pKa and ionization states of amino acids under physiological conditions.

Cysteine - ability to oxidize.

Polypeptides/proteins - amide bonds - electronic structure and geometry.

Primary structure - the 3 letter / 1 letter codes for amino acids and the convention for writing peptide sequences.

Importance of non-covalent interactions in biological systems.

Torsion angles. Hydrogen bonding in alpha helix and beta sheet, Ramachandran plots.

Tertiary structure - hydrophobic interactions, salt bridges, cystine, H bonds - combinations of helices and sheets.

Quaternary structure - protein-protein interactions.

Introduction to databases of protein sequences and structures.

Reaction free energy profiles, types of catalysis - general acid/base, nucleophilic catalysis.

Examples &ndash esterases, serine and cysteine proteases.

Introduction to cofactors/coenzymes/prosthetic groups.

Sugars - monosaccharides - structure and Fischer/Haworth projections.

Chemistry of hemiacetals, ring/chain equilibria. Pyranose and furanose forms. Anomers.

Glycosides, disaccharides - maltose, cellobiose.

Polysaccharides - linear and branching, cellulose, starch and glycogen.

Complex carbohydrates &ndash aminosugars, proteoglycans, glycosaminoglycans and peptidoglycans.

Nucleic acids - heterocyclic bases, H-bonding, base pairing (classical and non-classical).

Sugars - ribose, deoxyribose, in a biological context.

Phosphate esters &ndash reactions, kinetics and thermodynamics.

Nucleosides, nucleotides and the double helix (DNA vs. RNA conformation).

Polymerases - DNA replication, transcription and reverse transcription.

Chemical reactions of mutation and DNA repair processes.

Transcription and translation.

Introduction to recombinant DNA technology and molecular biology.

Essential Reading and Resource List

Foundations of Molecular Biology, C. M. Dobson, J. A. Garrard, A. J. Pratt, Oxford Chemistry Primers.

Lehninger Principles of Biochemistry, 4 th edition or later, David L. Nelson and Michael M. Cox, W. H. Freeman.

Fundamentals of General, Organic and Biological Chemistry, 5 th edition, John McMurry, Mary E. Castellion, David S. Ballantine, Pearson Prentice Hall 2007.


Biology Chapters 8 - 10

This chapter lays the foundations for the chapters on respiration and photosynthesis. Key concepts are as follows: The laws of thermodynamics govern energy transformations by living organisms, metabolic reactions couple energy-harvesting reactions to reactions that accomplish cellular work, and enzymes increase the rates of reaction. Understanding the properties of enzymes, how they work, and how their activities are regulated is necessary to achieve an understanding of metabolic pathways.

Rate of an enzyme-catalyzed reaction as a function of varying reactant
concentration, with the concentration of enzyme constant.

Activity of various enzymes at various temperatures (a) and at various pH (b).

The following questions are based on the reaction A + B ↔ C + D shown in Figure 8.1.

Succinate dehydrogenase catalyzes the conversion of succinate to fumarate. The reaction is inhibited by malonic acid, which resembles succinate but cannot be acted upon by succinate dehydrogenase. Increasing the ratio of succinate to malonic acid reduces the inhibitory effect of malonic acid.

A series of enzymes catalyze the reaction X → Y → Z → A. Product A binds to the enzyme that converts X to Y at a position remote from its active site. This binding decreases the activity of the enzyme.

The following questions are from the end-of-chapter "Test Your Understanding" section in Chapter 8 of the textbook.

Campbell's Biology, 9e (Reece et al.)
Chapter 9 Cellular Respiration and Fermentation

This is one of the most challenging chapters for students to master. Many students become overwhelmed and confused by the complexity of the pathways, with the multitude of intermediate compounds, enzymes, and processes. The vast majority of the questions in this chapter address central concepts rather than details of these pathways. Other questions have accompanying figures that provide details for reference and ask students to interpret or use these models. Overall, the emphases are on the inputs and outputs of each pathway, the relationships among these pathways, the cellular locations, redox as a central principle in respiration, and chemiosmosis.

Figure 9.2 The citric acid cycle.

In the presence of oxygen, the three-carbon compound pyruvate can be catabolized in the citric acid cycle. First, however, the pyruvate (1) loses a carbon, which is given off as a molecule of CO2, (2) is oxidized to form a two-carbon compound called acetate, and (3) is bonded to coenzyme A.

Exposing inner mitochondrial membranes to ultrasonic vibrations will disrupt the membranes. However, the fragments will reseal "inside out." These little vesicles that result can still transfer electrons from NADH to oxygen and synthesize ATP. If the membranes are agitated further, however, the ability to synthesize ATP is lost.

The following questions are from the end-of-chapter "Test Your Understanding" section in Chapter 9 of the textbook.

Campbell's Biology, 9e (Reece et al.)
Chapter 10 Photosynthesis

Students find this chapter quite challenging. Fortunately, some of the key concepts, such as chemiosmosis and redox, were discussed previously in the chapter on respiration and fermentation. The new key concepts are light as energy, light absorption and energy conversion by pigments, and linear and cyclic electron flow. Students are challenged to identify the relationships between the light reactions and the Calvin cycle, as well as the adaptive significance of C4 and CAM pathways. Comparison and contrast between photosynthesis and respiration, the significance of photosynthesis to Earth history and evolution of life, and the role of photosynthesis in global carbon cycles and environmental change are important topics to engage students.


1. Mnemonics

One of the best and oldest trips on learning how to memorize amino acids are using mnemonics devices. Mnemonic devices help speed up the process of memorization because it helps you brain to better encode and recall important details.

Essential Amino Acids Mnemonics:

The ten essential amino acids can be remembered as: PTV HIM TALL:

Hydrophobic Amino Acids Mneumonics:

Pro GAV PIL

Amino Acids with OH-Containing Side Groups

S-Containing Amino Acids

( U ) M ethionine

Basic Amino Acids

H istidine
A rginine

Amino Acids with Aromatic Side Groups

Nonpolar, Nonaromatic Amino Acids: AVGLIMP

Polar Amino Acids: STQNC

Aromatic Amino Acids: WYF

Positive Amino Acids: RKH

Negative Amino Acids: ED

Hydrophobic Amino Acids: FLAVI (like the virus)

Hydrophilic Amino Acids: REKHN (pronounced reckon)

2. Draw Them

Drawing (or coloring) the amino acids is actually going to help actually ingrain the knowledge versus a mnemonic device that will really only help you do well on the next test. There are 20 amino acids, so choose to draw one amino acid a day and you will have them all memorized within 3 weeks.

Because amino acids have the same basic structure, you really just need to remember their function group. After you know their function group, you just need to categorize them as polar, nonpolar, acid, or base.

Each time you write out the full name of the amino acid and draw the amino acid’s function group, write down the 3-letter code and 1-letter code. Try to think of ways that will help you remember these codes.

Here are some ways to remember some of the less obvious amino acid codes:

  1. Phenylalanine (pronounced like an f) = F
  2. Glutamine (pronounced like Q) = Q
  3. Aspartic Acid (pronounced AsparDic Acid) = D
  4. Arginine (sounds like arr -ganine) = R

The key in drawing these out is to learn how to memorize the amino acids through repetition and will help you to remember these acids well beyond the MCAT.

3. Use Amino Acid Flashcards

Using flashcards when studying for the MCAT can be a game changer, especially when it comes to memorizing the amino acids. Magoosh has free MCAT flashcards that include subjects: Organic Chemistry, Biology, and Physics. They even provide helpful mnemonics for learning new structures.

You can also check out these 24 free Amino Acids Flashcards from Varsity Tutors!


Physicochemical properties of amino acids

The 20 amino acids encoded directly by the genetic code can be divided into several groups based on their properties. Important factors are charge, hydrophilicity or hydrophobicity, size, and functional groups. [38] These properties are important for protein structure and protein–protein interactions. The water-soluble proteins tend to have their hydrophobic residues (Leu, Ile, Val, Phe, and Trp) buried in the middle of the protein, whereas hydrophilic side chains are exposed to the aqueous solvent. (Note that in biochemistry, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid.) The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them into the lipid bilayer. In the case part-way between these two extremes, some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. In similar fashion, proteins that have to bind to positively charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively charged molecules have surfaces rich with positively charged chains like lysine and arginine. There are different hydrophobicity scales of amino acid residues. [132]

Some amino acids have special properties such as cysteine, that can form covalent disulfide bonds to other cysteine residues, proline that forms a cycle to the polypeptide backbone, and glycine that is more flexible than other amino acids.

Many proteins undergo a range of posttranslational modifications, when additional chemical groups are attached to the amino acids in proteins. Some modifications can produce hydrophobic lipoproteins, [133] or hydrophilic glycoproteins. [134] These type of modification allow the reversible targeting of a protein to a membrane. For example, the addition and removal of the fatty acid palmitic acid to cysteine residues in some signaling proteins causes the proteins to attach and then detach from cell membranes. [135]

Table of standard amino acid abbreviations and properties

Two additional amino acids are in some species coded for by codons that are usually interpreted as stop codons:





















21st and 22nd amino acids
3-letter
1-letter

MW (weight)

Selenocysteine
Sec
U
168.064

Pyrrolysine
Pyl
O
255.313

In addition to the specific amino acid codes, placeholders are used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue. They are also used to summarise conserved protein sequence motifs. The use of single letters to indicate sets of similar residues is similar to the use of abbreviation codes for degenerate bases. [140] [141]























































































Ambiguous amino acids
3-letter
1-letter
Amino Acids Included
Codons Included
Any / unknown
Xaa
X
All
NNN

Asparagine or aspartic acid
Asx
B
D, N
RAY

Glutamine or glutamic acid
Glx
Z
E, Q
SAR

Leucine or Isoleucine
Xle
J
I, L
YTR, ATH, CTY (coding codons can also be expressed by: CTN, ATH, TTR MTY, YTR, ATA MTY, HTA, YTG)

Hydrophobic

Φ
V, I, L, F, W, Y, M
NTN, TAY, TGG

Aromatic

Ω
F, W, Y, H
YWY, TTY, TGG (coding codons can also be expressed by: TWY, CAY, TGG)

Aliphatic (non-aromatic)

Ψ
V, I, L, M
VTN, TTR (coding codons can also be expressed by: NTR, VTY)
Small

π
P, G, A, S
BCN, RGY, GGR

Hydrophilic

ζ
S, T, H, N, Q, E, D, K, R
VAN, WCN, CGN, AGY (coding codons can also be expressed by: VAN, WCN, MGY, CGP)

Positively charged

+
K, R, H
ARR, CRY, CGR

Negatively charged


D, E
GAN

Unk is sometimes used instead of Xaa, but is less standard.

In addition, many non-standard amino acids have a specific code. For example, several peptide drugs, such as Bortezomib and MG132, are artificially synthesized and retain their protecting groups, which have specific codes. Bortezomib is Pyz-Phe-boroLeu, and MG132 is Z-Leu-Leu-Leu-al. To aid in the analysis of protein structure, photo-reactive amino acid analogs are available. These include photoleucine (pLeu) and photomethionine (pMet). [142]


9.3: Exercise 1 - The 1-letter code for amino acids - Biology

Translation Theory : DNA ⇒ RNA ⇒ Protein

Life depends on the ability of cells to store, retrieve, and translate genetic instructions.These instructions are needed to make and maintain living organisms. For a long time, it was not clear what molecules were able to copy and transmit genetic information. We now know that this information is carried by the dioxyribonucleic acid or DNA in all living things.
DNA: DNA is a discrete code physically present in almost every cell of an organism. We can think of DNA as a one dimensional string of characters with four characters to choose from. These characters are A, C, G, and T. They stand for the first letters with the four nucleotides used to construct DNA. The full names of these nucleotides are Adenine, Cytosine, Guanine, and Thymine. Each unique three character sequence of nucleotides, sometimes called a nucleotide triplet, corresponds to one amino acid. The sequence of amino acids is unique for each type of protein and all proteins are built from the same set of just 20 amino acids for all living things.

Instructions in the DNA are first transcribed into RNA and the RNA is then translated into proteins. We can think of DNA, when read as sequences of three letters, as a dictionary of life.
Aim: Convert a given sequence of DNA into its Protein equivalent.
Source: Download a DNA strand as a text file from a public web-based repository of DNA sequences from NCBI.The Nucleotide sample is ( NM_207618.2 ), which can be found here.To download the file :


Steps: Required steps to convert DNA sequence to a sequence of Amino acids are :

Coding Translation

The very first step is to put the original unaltered DNA sequence text file into the working path directory.Check your working path directory in the Python shell,

Next, we need to open the file in Python and read it. By default, the text file contains some unformatted hidden characters. These hidden characters such as “/n” or “/r” needs to be formatted and removed. So we use replace() function and get the altered DNA sequence txt file from the Original txt file.


Watch the video: How to remember 1 letter amino acid code. how to remember single letter amino acid abbreviation (July 2022).


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