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Nitrogen Compounds Flashcards

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Organic Chemistry 101 flashcards
1
Q

Shape of the amine?

A

Primary
Secondary
Tertiary:

Trigonal planar

Quaternary ammonium ion:

Tetrahedral

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2
Q

Difference between phenylamine and phenylmethylamine?

A

Phenylamine has -nh2 group directly bonded to the benzene ring

Structural formula:
C6h5NH2

C6H5CH2NH2

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3
Q

Trend of boiling point:

A

Increases as the number of carbon atom increases

Strength of van der waals’ forces between molecules increases with increasing number of electrons.
(Same as other compounds)

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4
Q

For isomeric amines, what are the two factors affecting their boiling point?

Note: (id-Id

A

Hydrogen bonding:

PRIMARY AND SECONDARY AMINES form stronger hydrogen bonds between their molecules whereas TERTIARY only can form weaker van der waals forces.

(Primary amines have protonic hydrogen)

Permanent-dipole-permanent-dipole interactions

  1. POLAR amine molecules will have stronger pd-pd interactions between the molecules while other amine molecules only have id-Id interactions
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5
Q

Is amines soluble in water and why? What is trend of solubility as number of carbon increases

A

Yes. Ability to form hydrogen bonds with water.

Protonic hydrogen is now the H bonded to the O atom in the water molecule. (thus tertiary amines can be soluble in water)

Solubility decrease as number of carbon atom increases
Bulky, non-polar groups hinders formation of hydrogen bonds between amines and water molecule

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6
Q

Why can amines act as a base?

A

Availability of a lone pair of electrons on its N atom for protonation. It accepts the proton by forming a dative covalent bond with it.

RNH2 + H2O RNH3+ + OH-

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7
Q

Base strength of amines depend on:

Name 2

A

Availability of lone pair of electrons on N atom for protonation

Relative stability of the resultant cation formed

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8
Q

Factors that affect the availability of lone pair of electrons on N atom for protonation:

A

Presence of electron-donating groups:
Makes the lone pair of electrons on N atom of amine more available for protonation.

Presence of benzene ring:
P orbital of N atom overlaps with the pi electron cloud of the benzene ring. Lone pair of electrons on N atom is delocalised into benzene ring. –> less available for protonation.

Presence of electron-withdrawing groups:

Make the lone pair of electrons on N atom of amine less available for protonation.

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9
Q

Why does primary and secondary amides form dimers in their liquid phase?

A

Because amine has both the protonic hydrogen and a lone pair on a highly electronegative atom. Can form hydrogen bonds between the molecules.

Note: tertiary amides do not have protonic hydrogen

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10
Q

Is amide a base or an acid?

A

NONE.

Amide do not act as bases and are neutral to litmus in aqueous solution.

The p orbital of N atom overlaps with the pi electrons cloud of the neighboring carbonyl group. The lone pair of electrons on N atom is delocalised into the carbonyl group and not available for protonation.

(Very similar explanation to why phenylamine is weaker base than NH3)

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11
Q

What is amino acid?

A

Contains at least one amino group (NH2) and one carboxyl group (COOH)

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12
Q

Name and structure of commonly found human proteins.

A

a-amino acids where the NH2 group is directly bonded to the a-carbon

NH2CHRCOOH

Different amino acids have a different R group.

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13
Q

What is zwitterion? How does it form?

A

Species that has both positively and negatively charge groups is called a zwitterion.

Form that amino acids exist as in aqueous and solid state.

Amino acid undergo intermolecular acid-base reaction so that NH2 group gains a proton to become NH3+ and COOH lose a proton to become COO-.

Can have more than one NH2 or COOH group if the R group is NH2 or COOH group

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14
Q

Optical isomerism of amino acid?

A

All chiral except for glycine.

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15
Q

Melting point of amino acid?

A

High melting point

Strong electrostatic forces of attraction between oppositely charged groups of the zwitterion

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16
Q

Solubility in water

Note: 2 ways to be soluble in water

  1. Hydrogen bonding
  2. Ion-dipole interaction with water
A

Amino acid is soluble in polar solvent and not soluble in non-polar solvent.

Zwitterion forms ion-dipole interaction with water molecules. (Read chem-bonding)

No effective interactions between the ions and molecules of non-polar solvent.

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17
Q

Is amino acid a base or an acid?

A

BOTH.
Amino acid are amphoteric.

In acidic conditions, amino acid acts as a base and accepts a proton to form cation. (Add to COO-)

Zwitterion + H+ —> NH3+CHRCOOH

In basic conditions, amino acid acts as a acid and donates a proton to form anion (remove from NH3+)

Zwitterion + OH- —> NH2CHRCOO- + H2O

18
Q

How to determine to structure of amino acid at different PH?

A

If the PH is smaller than the Pka, the protonated form of the group remain dominant.
If PH is larger than the Pka, the deprotonated form of the group become dominant
(Note: R group, nh2 and COOH group all have different Pka values)

19
Q

Isoelectric point?

A

Particular PH at which an amino acid exists solely in its zwitterion if form with net charge of zero on the species.

Not migrate under the influence of electric field

20
Q

How does amino acid acts as buffers?

A

When a small amount of acid is added,

Zwitterion + H+ —-> NH3+CHRCOOH

when a small amount of alkali is added

Zwitterion + OH- —> NH2CHRCOO- * H2O

(Because zwitterion is amphoteric it can react with the small amount of acid and alkali so that there would be minimal change in PH)

21
Q

Functions of proteins?

A

The primary structure determines the three-dimensional shape of the protein that is crucial in helping the protein does it function.
E.g collagen resembles a rope which is great for providing support

Structural protein for support

Transport protein for transporting of other substances

Hormonal protein for the coordinates of activities in the body

Defensive protein for the protection against diseases

Catalytic protein for the acceleration of certain chemical processes

22
Q

How does protein molecule form?

Note: structural formula must be in the same sequence as the naming.

A

Involves the formation of peptide bonds(aka amide linkage or amide bond) via condensation reaction between carboxyl group of one amino acid and amino group of another acid. A molecule of water is removed from the reaction

Remove OH from one amino acid and H from another and combine 2 acid together to form a peptide bond and H20

Possess free amino group on one side and free carboxyl group on the other side for further condensation reaction.

23
Q

Definition of:
Dipeptide
Tripeptide
Tetrapeptide

A

Made from (N) amino acids and contains (N-1) peptide bonds

E.g
Tetrapeptide is made from four amino acid and contain three peptide bond.

24
Q

Definition of
polypeptide
Polypeptide backbone
side-chains:

A

Polypeptide are peptide of longer chain length
Polypeptide backbone consists of repeating units of -NHCHCO

Side chain are the R groups of amino acid residues(an amino acid unit in the polypeptide chain)

By convention, the free amino group is always on the left and free carboxyl group is on the right.

25
Q

Does the R group get protonated/deprotonated?

Whet are the exceptions?

A

Yes.

CONH2 as the R Group does not get protonated because amide is neutral

26
Q

Acidic/alkaline Hydrolysis of polypeptide

Conditions:
Mechanism:

Enzymatic hydrolysis
Conditions:
Mechanism:

A

Conditions:
(Acidic) H2S04 or HCL heat for several hours
(Alkaline) NaOH(aq) heat for several hours

Mechanism: (breaks the peptide bond (CONH) in the polypeptide) and convert them back to individual amino acid)
+ if it’s acidic: the amino acid will be protonated
+ if it’s alkaline: the amino acid will be deprotonated
(Including the R groups

Without heating, the peptide bond is not broken)
Condition: pepsin(aq) at suitable temperature
Mechanism: break the peptide bond and add OH back to the C=O bond and add H back to the N-H bond

27
Q

Definition:

Primary structure

A

Amino acid sequence of the poly-peptide chain

28
Q

How to find out the primary structure of protein?

A

Undergo partial hydrolysis to find the smaller peptide units to figure out the sequences

E.g here are 3 dipeptides after partial hydrolysis

A-A
B-B
A-B

A must be paired with A and also with B
B must be paired with B and also with A

Therefore:
Structure;
A-A-B-B

(If the amino acid is bonded to 4 different amino acid means that it is likely to appear twice in the polypeptide)

29
Q

Define secondary structure:

A

Regular coils and folds in localized segments of the polypeptide chain as stabilized by hydrogen bonding between the backbone C=O and N-H groups of the poly-peptide chain.

30
Q

Define a-helix:

A

Is a regular spiral configuration of the polypeptide chain which is stabilized by hydrogen bonding between the backbone c=o group of one amino acid residue and the backbone N-H group of the 4th amino acid residue further down the chain.

(within the molecule)

31
Q

Define b-pleated sheet:

A

Consists of adjacent polypeptide strands stabilized by backbone c=o group of one strand and backbone N-H group of another adjacent strand

32
Q

Sketching both a-helix and b-pleated sheet:

A

Draw a regular coil to represent the polypeptide backbone of a-helix + one hydrogen bond between C=O and N-H and labelled

Draw the polypeptide strand in zig-zag manner and the 2 strands should be shifted so that C=O bond matches the N-H bond + label and draw the hydrogen bond

33
Q

Tertiary structure:

A

Three-dimensional shape of a polypeptide as stabilized by the R group interactions

34
Q

What are the 4 types of R group interactions

A

Ionic interactions between charged R groups e.g NH3+ and COO- groups(depends on the PH)

Hydrogen bond between polar groups capable of forming hydrogen bonds e.g OH, CONH2 NH2 and COOH(depends on PH, it can be either ionic interactions or hydrogen bond)

Disulfide bridge(S-S bond) between thiol group (S-H)

Van der waals forces between non-polar groups e.g alkyl,aryl group and SCH3 residue

35
Q

What is a globular protein?

A

A compact, roughly spherical structure caused by folding of poly-peptide chain.

Poly-peptide chain folds because of non-polar groups that repel water environment and polar groups that interact with water hence:

Non-polar groups located at the interior and polar groups at the exterior

36
Q

define Quaternary structure:

A

Spatial arrangement of two or more polypeptide chain stabilized by R group interactions to form a large complex protein molecule.

37
Q

Describe the protein components of hemoglobin?

Insulin also have two polypeptide chain stabilized by disulfide bridges

A

Hemoglobin contains 2 a-chain and 2 b-chain subunits held by R group interactions(except for disulfide bridge)

Each subunit is bonded to a haem residue which contains Fe2+ capable of binding to oxygen(since there is 4 subunits can take 4 oxygen molecules to form oxyhaemoglobin in the lungs)

38
Q

Enzymes:

Functions:
How does it work:
Example(hydrolysis)

A

There enzymes provides an active site for the substrate to bind to and reaction occurs.

The shape of the active site is determined by the tertiary structure of the enzymes and this shape only fits a specific substrate.

E.g pepsin provides an active site for the protein substrate to bind to and help water molecules bond to the polar carbonyl group

39
Q

What is denaturation?

A

Protein loses its shape and unfold into random coils–> loses its function

Involves the disruption and destruction of secondary and tertiary structure of protein. (Either it affects the R group interaction or the hydrogen bond between the C=O and N-H backbone groups.)

Primary structure remain intact as denaturation reaction are not strong enough to break peptide bonds.

40
Q

Ways to denature a protein?

Give me 4

A
  1. Extreme heat
    Supplied heat increase KE and give them sufficient energy to overcome the weak van der waals forces and hydrogen bond in the secondary or tertiary structure of protein.
  2. Extreme PH
    A suitable PH is required such that both R groups are in ionic form for ionic interaction and NH2 and COOH form for hydrogen bonds.
    E.g optimal PH for pepsin is 2
    However At low PH, NH2 becomes NH3 and at high PH COOH becomes COO- (disrupts hydrogen bond)
    At low PH, COO- becomes COOH and at high PH, NH3+ becomes NH2 (disrupts ionic bond)
    (Depending on the R group, different disruption of bonds)
  3. Heavy metal ions
    Heavy metal ions form ionic interactions with COO- which brings about formation of insoluble protein salts. (Disrupts ionic interaction)
    It also has high affinity with sulfur and bind tightly to SH group (disrupts disulfide bridges)
  4. Alcohol
    Disrupts the hydrogen bond in the secondary and tertiary structure of the protein since it also forms hydrogen bond with the protein. (Recall that protein is stabilized by hydrogen bonding)
41
Q

What is an amine?

Hint: general formula

A

Primary amines:

RNH2

Secondary amines:

RNHR1

Tertiary amines:

RNR1R2

Quaternary ammonium ion:

R1NR2R3
(stands for + charge)

Nitrogen Compounds (1 decks)

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