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ORGANIC NITROGEN COMPOUNDS - Coggle Diagram
ORGANIC NITROGEN COMPOUNDS
Amines & heterocycles
Basis
Amines are made up of an sp3 hybridized nitrogen and are either alkyl substituted or aryl substituted
Amines are classified as primary, secondary, or tertiary based on the number or organic substituents directly attached to the nitrogen
secondary
tertiary
primary
Nomenclature
Primary amines are named in two main ways using the IUPAC system.
Symmetrical 2o and 3o amines are named as alkylamines and the prefix di- or tri - added to indicate the number of substituents.
Unsymmetrical 2o and 3o amines are named with the largest chain being the base chain (prefix+yl+amine)
Structure and properties
The nitrogen atom in most amines is sp3 hybridized.
Due to their tetrahedral configuration, amines with three different substituents are chiral.
During the inversion, the sp3 hybridized amine momentarily rehybridizes to a sp2 hybridized
Boiling points and Water solubility
Methyl, dimethyl, trimethyl, and ethyl amines are gases under standard conditions. Most common alkyl amines are liquids, and high molecular weight amines are, quite naturally, solids at standard temperatures.
Most aliphatic amines display some solubility in water, reflecting their ability to form hydrogen bonds.
A large and widespread class of naturally occurring amines is known as alkaloids
Alkaloids include compounds that may be classified as antimicrobial (quinine), as analgesics (morphine, codeine), as hallucinogens (mescaline, LSD), and as topical anesthetics (cocaine).
Basicity of Amines
The lone pair electrons makes the nitrogen in amines electron dense
Amine are basic and easily react with the hydrogen of acids which are electron poor
Amines react with water to establish an equilibrium where a proton is transferred to the amine to produce an ammonium salt and the hydroxide ion
Just as the acid strength of a carboxylic acid can be measured by defining an acidity constant Ka. the base strength of an amine can be measured by defining an analogous basicity constant Kb.
Weaker Base = Larger Ka and Smaller pKa of the Ammonium ion
Stronger Base = Smaller Ka and Larger pKa of the Ammonium ion
Inductive effects in Nitrogen Basicity
Alkyl groups donate electrons to the more electronegative nitrogen.
The inductive effect makes the electron density on the alkylamine's nitrogen greater than the nitrogen of ammonia.
The small amount of extra negative charge built up on the nitrogen atom makes the lone pair even more attractive towards hydrogen ions
Basicity of Arylamines
Basicity of Aniline
Aniline is substantially less basic than methylamine pKa
the lone pair of electrons on the nitrogen are delocalized by the aromatic p system,
The lone pair electrons of aniline are involved in four resonance forms making them more stable
Basicity of Substituted Arylamines
The addition of substituents onto the aromatic ring can can make arylamines more or less basic.
Substituents which are electron-withdrawing (-Cl, -CF3, -CN, -NO2) decrease the electron density in the aromatic ring and on the amine making the arylamine less basic
Substituents which are electron-donating (-CH3, -OCH3, -NH2) increase the electron density in the aromatic ring and on the amine making the arylamine more basic.
Biological Amines & the henderson-Hasselbach Equation
The Henderson-Hasselbalch equation: pH = pKₐ + log([A⁻]/[HA]).
We used the Henderson-Hasselbalch equation to show that under physiological pH, carboxylic acids are almost completely dissociated into their carboxylate ions.
Biomolecules : Amino acids, peptides & proteins
Structures of Amino Acids
Amino acid are disfunctional molecules
Two forms possible
Uncharged
Zwitterion
molecular chemical species with one unit electric charges of opposite signs and usually located on non-adjacent atoms
present in aqueous solution
Behaviour
Soluble in water
insoluble in hydrocarbures
amphiprotic
Alanine is a simple amino acid
There are all α amino acid: the one next to the carbonyl group
19/20 are primary amines
There are 20 common amino acids found in proteins
Classification which is depending on the structure of the side chain
acididic
basic
Neutral
2 more are found in some organism
700 are found in the nature
11/20 can be synthetized by the body= nonessential amino acids
9/10 are not = essential amino acids
Amino Acids and the Henderson–
Hasselbalch Equation: Isoelectric Points
equation giving the pH of a buffered system
If we know the pH and the pKa of an mino acid, then we can calculate the ratio of [A-] and [HA] in the solution
Isoelectric point
This is the pH where we can find the zwitterion form.
Above, we find the deprotonated
Under, we find the protonated
Synthesis of Amino Acids
the Hell–Volhard–Zelinskii reaction
The Amidomalonate Synthesis
Reductive Amination of a-Keto Acids
Enantioselective Synthesis
Peptides and Proteins
Amino acid polymers
The bond between each amino acild that makes the peptide is called the
protein's backbone
which is an amide bond
Amide nitrogen is non basic because the interaction between the carbo,nyl group delocalizes the unshared electron
The p orbital of the nitrogen overlaps the p orbital the carbonyl group. It gives to C-O bond the same behaviour as a double bond and limits the rotation around it.
The amide bond is planar and N-H bond is oriented 180° to the C=O bond
Conventionally
peptide are writtten with the
N-terminal on the left
with the free NH3+
and C-terminal on the right
with the free CO2- group
Abreviation = (Ser-Ala)
individual amino
acids are called residues
the covalent bond RS-SR between 2 cysteine
mild oxidation of a thiol
Amino Acid Analysis of Peptides
This analysis is based on the work of William Stein and Stanford Moore who received the nobel prize in 1972
Preparation of the sample:
petpides are broken into amino acids by S2N reaction with iodoacetic acid and then amid bond are hydrolyzed by heating with 6 M HCl at 110 °C for 24 hours
The goal is to reduce all the disulfide bonds and to cap SH groups of cysteine residues
Then the mixture is separated by using the chromatpgraph technique
high-pressure liquid chromatography
(HPLC)
In both; the mixture is dissolved is a solvent (mobile phase)
It goes through an adsorbent material (stationary phase)
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or ion-exchange chromatography.
This technique uses a compound called ninhydrin that reacts quickly with the amino acid and gives a purple colour. This colour is detected by a spectrometer and the intensity gives the quantity of amino acid
Peptide Sequencing:
The Edman Degradati
What It is ?
to find the order of amino acid in the peptide
Another main technique mass spectrometry which useselectrospray ionization (ESI)/ matrix-assisted laser desorption ionization
(MALDI) linked to a time-of-flight (TOF) mass analyze
How ?
This technique consists in separating an amino acid from the end of a peptide chain
The amino acid separated is identified and the technique is repeated with the next new amino acid at the terminal position
This operation can be done automatically, quickly up to 50 repetitive sequencing cycle
Edman degradation
pathway
Biomolecules: Nucleic acids
Nucleotides & nucleic acids
5 bases in nucleotid acids
Adenine (A), guanine (G), cytosine (C), Thymine (T) and Uracile (U)
A,C,G,T in ADN, A,C,G,U in ARN
Bases are Pyrimidines and Purines
Pyrimidine
Purine
the based is linked to the pentose sugar with a bond between C1 of pentose sugar & N1 of pyrimidine base of N9 of purine base
the pentose sugar is 2-deoxyribose in DNA and ribose in RNA
Nucleotide = nucleic acid base + pentose sugar + inorganic acid (phosphoric acid)
Nucleotides are units of DNA & RNA but also have other functions
ADP & ATp (adenosine di & triphosphate) : role in cell metabolism
coenzymes like FAD (flavin adenine dinucleotide) contain adenine nucleotide as component
nucleotides joined together by link between phosphate group of one nucleotide and OH group on 2rd carbon of the sugar unit of the other nucleotide
writing sequence of nucleotides: starting from 5'end to 3'end
5'end= nucleotide having a free phosphate group
3'end= final nucleotide having a free OH group on his 3' crabon
Base-pairing in DNA, Watson-Crick model
DNA backbone is polar & charged : it's a polyanion
DNA is double-stranded with strands running in opposite directions : 5'-3' and 3'-5'
trands held together with H bonds between complementary bases
G forms 3 H-bonds with C
T forms 2 H-bonds with A
G-A orT-C H-bonds impossible
DNA replication
nucleus contains all necessary components required for the replication : a synthesis of a new ADN
The 2 strands of ADN are separated by disrupting H-bonds
The enzyme DNA polymerase recognize each base and associate a free nucleotide to it
DNA polymerase also helpsthe formation of the ester bond between 5' phosphate group of the existing nucleotide and 3'OH end of the new one
each strand is used to produce a new DNA starnd
replication always goes from 5' to 3' part of the existing DNA
DNA transcription
RNA types
mRNA : Messenger RNA : carries genetic information from DNA in the nucleus to the cytoplasm where proteins will be synthetized
tRNA : Transfer RNA read the code carried by mRNA. This process is translation
rRNA : Ribosomal RNA : describes RNA molecules which make up with proteins the ribosome which will wynthetize proteins
RNA synthesis is called transcription
RNA is built from ribonucleotides
DNA strand used for transcription is the template strand
DNA complementary strand is called coding or informational strand
DNA strands strat unwinding and ribonuleotides come to this area
RNA synthesis goes fom 5' to 3'
DNA thymine needs RNA adenine, DNA cytosine : RNA guanine, DNA guanine : RNA cytosine but DNA adenine needs RNA URACIL
When RNA synthesis is done, it is released and DNA helix is reformed
nucleotide sequence of RNA syntetized is identical to the coding DNA strand sequence (except U replacing T)
Application : acrylamide formation
what is acrylamide ?
chemical formula C₃H₅NO
2A class : probably carcinogenic to humans in CMR classification (carcinogenic/mutagenic/toxic to reproduction)
found in french fries, café, grilled bread...
found in foods rich in starch and asparagine when cooked at temperatures above 120°C
Not present in the initial food but created during processing
How is it formed ?
exemple of rye-acrylamide formation with Maillard-reaction
concerns
French agency Anses reeavulated in 2011 French people exposition to acrylamide. This exposition decreased of 14% for adults and 45% for children since 2005
But, these exposure levels are very close to the carcinogenic for animals levels
Maillard reaction
Excellent examples of the Maillard reaction are the crust of roast pork or baked bread. The Maillard reaction also creates, besides colour, countless complex flavours at the same time. The sulphur-containing amino acids methionine and cysteine play a primary role within the formation of the flavour-intensive components gained during the Maillard reaction.
The reaction is continuous and very reactive intermediate substances are formed which subsequently react in several different ways. Eventually, a furan derivate is gained and this derivate reacts with other components to polymerize into a dark-coloured insoluble material containing nitrogen. The Maillard reaction also takes place at room temperature but at a much slower rate and occurs at its slowest at low temperatures, low pH and low Aw levels
The Maillard reaction, named after L. C. Maillard, is also known as non-enzymatic browning. It is an extremely complex process and is the reaction between reducing sugars and proteins by the impact of heat. The Maillard reaction starts with the reaction of a reducing sugar with an amine, creating glycosylamine. These substances undergo a reaction called Amadori rearrangement to produce a derivate of amino deoxy fructose.
The flavour of such roasted or grilled meats also contains heterocyclic compounds derived from amino acids, nucleotides and sugars from the Maillard reaction such as oxopropanol and hydroxymethylfurfural. Unsaturated fatty acids, as well as aldehyde–fatty–acid components, also contribute to the formation of odorous heterocyclic flavour compounds during the Maillard reaction.
