Protein And A.A

Question 1

Function of protein?

Answer 1

Static : maintain structure and strength of body. Eg; elastin, collagen in 🦴, vascular system, alpha keratin in epithelium tissue, keratin (present in hair, wool, and silk) and myosin (present in muscles), etc

Dynamic: working house 🏠 of cell
Enzymes, hormone, blood clotting factors, immunoglobulin, receptor, genetic control 🧬, muscle 💪 contractions, respirations etc

Question 2

Standard amino acids

Answer 2

20 aa that found in protein structure

Question 3

Amino acids?

Answer 3

Organic compounds with
2 functional group= amino( -NH2) & carboxyl (-COOH)

H– CH–COOH
|
NH2

It has 4 group attached with carbon
R, H, COO-, NH3+

Question 4

Optical isomer of aa? 📀

Answer 4

A carbon attached with 4 different groups (Asymmetric) show optical isomer.
✍️ By L- and D- Amino acid based on configuration

Question 5

Essential aa

Answer 5

Arginine. 
Valine
Histidine
Leucine
Tryptophan 
Iso leucine

Lysine
Methionine
Phenylalanine
Threonine

PVT TIM HALL
phenylalanine
Valine
Tryptophan
Threonine
Iso leucine
Methionine 
Histidine
Arginine
Leucine 
Lysine

Question 6

Metabolic fate of amino acids?

Answer 6

1. Glycogenic aa: glucose or glycogen can synthase

2. Ketogenic aa: fat

Question 7

structure of proteins?

Answer 7

primary: linear sequence of aa
backbone of protein
secondary: conformat

Question 8

1. Primary Structure of Protein ?

Answer 8

1. Primary Structure of Protein
   The Primary structure of proteins is the exact ordering of amino acids forming their chains.
   The exact sequence of the proteins is very important as it determines the final fold and therefore the function of the protein.
   The number of polypeptide chains together form proteins. These chains have amino acids arranged in a particular sequence which is characteristic of the specific protein. Any change in the sequence changes the entire protein.

Question 9

pronase ?

Answer 9

non specific proteolytic enzyme that cause complete hydrolysis of protein.

Question 10

how to separate and estimate of AA

Answer 10

separation by hydrolysis

estimate by chromatography

Question 11

how to degrade protein into small fragment?

Answer 11

1. liberation of protein:
   a. urea & guanidine hydrochloride = break non covalent bond == from peptide unit
   b. performic acid== cleave disulfide bond btw polypeptide unit

2. no. of polypeptide: 
dansyl chloride== bind with N-terminal aa= from dansyl polypeptide = hydrolysis of polypeptide = equal amount of  dansyl aa
3. breakdown of polyp. into fragment: 
a. enzymatic
b. chemical method

Question 12

sequence determination of aa?

Answer 12

Sanger’s reagent:
1-fluoro 2,4 dinitro-benzene [FDNB] = determine insulin sequence
FDNB + N terminal AA —– hydrolysis—–D.N.phenyl -N.terminal AA

Edam’s regent:
Phenylisothiocyanate (PITC)+
N-terminal amino acid ——N-terminal PTC [ p. thiohydantoin] derivative.===== determine by HPLC

Question 13

overlapping peptide

Answer 13

overlapping peptide library can be used for linear or continuous epitope mapping, which can be used to figure out which part of a given protein or peptide contains the essential amino acids that .
Overlapping peptide libraries are generated by dividing the original protein or peptide sequence into many overlapping peptides of the same length. They are defined by peptide length and peptide offset.

Question 14

polar amino acids?

Answer 14

The polar amino acids include:
arginine, asparagine, aspartic acid (or aspartate), glutamine, glutamic acid (or glutamate), histidine, lysine, serine, and threonine.
Polar side chains contain groups that are either charged at physiological pH or groups that are able to participate in hydrogen bonding.

Question 15

Nonpolar amino acids?

Answer 15

Nonpolar amino acids include alanine (Ala), leucine (Leu), isoleucine (Ile), proline (Pro), tryptophan (Trp), valine (Val), phenylalanine (Phe), and methionine (Met).
The side chains of these amino acids are long carbon chains or carbon rings, making them bulky. They are hydrophobic, meaning they repel water.

[A nonpolar molecule has no separation of charge, so no positive or negative poles are formed. In other words, the electrical charges of nonpolar molecules are evenly distributed across the molecule. Nonpolar molecules tend to dissolve well in nonpolar solvents, which are frequently organic solvents.

Question 16

secondary structure of protein type?

Answer 16

conformation of twisted or folded polypeptide

alpha helices, beta sheets, and beta turns.

Question 17

alpha helix

Answer 17

1. tightly packed coiled structure
2. h-bond between [N-H]–[O=C]
3. each turn = 3.6 aa
   distance btw turn = 0.54 mm
   spacing of each aa= 0.15mm
   4.stable by h-bond
4. right handed alpha helix = more stable

Question 18

Basic AA?

Answer 18

There are three amino acids that have basic side chains at neutral pH.
These are arginine (Arg), lysine (Lys), and histidine (His).

Question 19

ACIDIC AA?

Answer 19

Those whose side chains can carry a negative charge at certain pH values. Typically aspartic acid, glutamic acid

Question 20

aromatic amino acids ?

Answer 20

Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids

Question 21

Beta sheets

Answer 21

Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet.

Question 22

parallel beta sheet vs antiparallel vs mixed sheets?

Answer 22

Parallel beta sheet - All bonded strands have the same N to C direction.
antiparallel sheets they all run in opposite directions.
In mixed sheets some strands are parallel and others are antiparallel.

Question 23

bonds in protein

Answer 23

1. covalent bond
    peptide and disulfide bond [--CH2-S-S-CH2--.]
2. non-covalent bond
  h-bond
  hydrophobic bond 
  electrostatic bond
 van der waal

Question 24

method of determining protein structure?

Answer 24

the main techniques used to determine protein 3D structure are X-ray crystallography and nuclear magnetic resonance (NMR).

Question 25

METHOD OF PURIFICATION OF PROTEIN

Answer 25

Protein purification is a series of processes intended to isolate one or a few proteins from a complex mixture, usually cells, tissues or whole organisms

Ion Exchange Chromatography. 
HPLC
GEL-chromatography
electrophoresis
immuno-electrophoresis
iso-electric focusing

Question 26

Isoelectronic point of aa?

Answer 26

The isoelectric point of an amino acid is the point at which the amino acid has no net electrical charge. It is an important characteristic for any amino acid, because every amino acid has at least two acid–base (titratable) groups.

Question 27

zwitterion

Answer 27

A zwitterion is a functional group molecule in which at least one has a positive electrical charge and one a negative electrical charge. The whole molecule’s net charge is negative. The best-known examples of Zwitterions are amino acids. They have a group of amines (basic) and a group of carboxyls (acidic)