Protein And A.A Flashcards
Function of protein?
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
Standard amino acids
20 aa that found in protein structure
Amino acids?
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+
Optical isomer of aa? 📀
A carbon attached with 4 different groups (Asymmetric) show optical isomer.
✍️ By L- and D- Amino acid based on configuration
Essential aa
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
Metabolic fate of amino acids?
- Glycogenic aa: glucose or glycogen can synthase
2. Ketogenic aa: fat
structure of proteins?
primary: linear sequence of aa
backbone of protein
secondary: conformat
- Primary Structure of Protein ?
- 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.
pronase ?
non specific proteolytic enzyme that cause complete hydrolysis of protein.
how to separate and estimate of AA
separation by hydrolysis
estimate by chromatography
how to degrade protein into small fragment?
- 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
sequence determination of aa?
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
overlapping peptide
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.
polar amino acids?
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.
Nonpolar amino acids?
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.
secondary structure of protein type?
conformation of twisted or folded polypeptide
alpha helices, beta sheets, and beta turns.
alpha helix
- tightly packed coiled structure
- h-bond between [N-H]–[O=C]
- each turn = 3.6 aa
distance btw turn = 0.54 mm
spacing of each aa= 0.15mm
4.stable by h-bond - right handed alpha helix = more stable
Basic AA?
There are three amino acids that have basic side chains at neutral pH.
These are arginine (Arg), lysine (Lys), and histidine (His).
ACIDIC AA?
Those whose side chains can carry a negative charge at certain pH values. Typically aspartic acid, glutamic acid
aromatic amino acids ?
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids
Beta sheets
Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet.
parallel beta sheet vs antiparallel vs mixed sheets?
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.
bonds in protein
1. covalent bond
peptide and disulfide bond [--CH2-S-S-CH2--.]
2. non-covalent bond
h-bond
hydrophobic bond
electrostatic bond
van der waalmethod of determining protein structure?
the main techniques used to determine protein 3D structure are X-ray crystallography and nuclear magnetic resonance (NMR).
METHOD OF PURIFICATION OF PROTEIN
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
Isoelectronic point of aa?
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.
zwitterion
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)
