Nitrogen Compounds Flashcards

Question

Does the R group get protonated/deprotonated? Whet are the exceptions?

Answer 1

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

Answer 2

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

Answer 3

Amino acid sequence of the poly-peptide chain

Answer 4

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)

Answer 5

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.

Answer 6

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)

Answer 7

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

Answer 8

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

Answer 9

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

Answer 10

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

Answer 11

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

Answer 12

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

Answer 13

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)

Answer 14

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

Answer 15

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.

Answer 16

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)

Answer 17

Primary amines: RNH2 Secondary amines: RNHR1 Tertiary amines: RNR1R2 Quaternary ammonium ion: R1N*R2R3 (*stands for + charge)