Amino Acids and Proteins Part 2

hey guys me again, this is just a continuation from the post proteins and amino acids

Organizations in Proteins

Primary structure refers to the number and sequence of amino acids in the polypeptide chain. This is very important because the juxtaposition of the R group COOH and the NH determines how the protein folds. They only bond maintaining this structure is the covalent peptide bond between these acids.


Secondary structure refers to the way the polypeptides turn or fold upon itself as a result of hydrogen bonding. This results in a more stable and robust structure than a straight chain. There are two types of structures alpha helix and beta pleated sheet.

The alpha helix is the form found in the protein keratin (found in hair, nails, and feathers). This polypeptide chain is twisted into a helix like an extensible telephone cord; successive turns of the helix are linked together by weak hydrogen bonds situated between the amino groups of one term and the carboxyl group of the next.

H bond bond with the carboxyl group of 1 amino acid and he NH group of and amino acid residue 3.6 units away.

The beta pleated sheet is an arrangement of a number of adjacent polypeptide chains running anti-parallel to each other. The neighbouring chains are joined together by hydrogen bonds between C=O and NH groups of one chain and the C=O and NH groups of the adjacent chain. All NH and C=O groups are involved in hydrogen bonding. This arrangement gives a high tensile strength with no stretch. Example silk fibroin is a protein that is entirely beta pleated. Some proteins have regions of beta pleated sheet. The individual chains can pack closely together as the R groups are usually small.



Tertiary structure is the way a polypeptide folds and foils to form a complex molecular shape as a result of bonds formed between the R groups.

Between R groups:

—NH3+ ——COO- ionic bonds

—H————O=C    hydrogen bonds

—S————S          disulphide bonds

—between large ring structures, hydrophilic interactions (van der waal forces)


This interaction causes the protein to fold into a precise compact globular shape with the hydrophobic parts on the inside and the hydrophilic parts on the outside. For some proteins this means that a single molecule can be surrounded by a shell of water molecules and become separated thereby making them soluble. Most enzymes fall into this category that is they are globular proteins which are capable of dissolving and catalyzing reactions within a cell.




Quaternary structure is only present when proteins consist of two or more polypeptide chains. It refers to the way in which these polypeptides are arranged to form a biologically active protein. E.g. hemoglobin.



Properties of Proteins


Denaturation – this is the loss of the specific 3-D conformation of a protein. The change can be temporary or permanent and he sequence of the amino acid remains unaffected. The molecule can no longer perform its biological function. Several agents causes denaturation

  • Heat or radiation:- causes the molecule to vibrate violently disrupting hydrogen and ionic bonds.
  • Strong acids, alkalis, high concentration of salts: – disrupts ionic bonds. Peptide bonds may break if left for a long time.
  • Heavy metals: – cations form strong bonds with ionized carboxylic groups disrupting ionic bonds.
  • Urea:- competition for hydrogen bonds, precipitation of soluble proteins. High concentrations of urea molecules denature proteins by allowing water molecules to solvate non-polar groups in the interior of the protein.
  • Agitation: – shearing of hydrogen bonds, beating of egg white albumin into a meringue.
  • Organic solvents and detergents i.e.

Chaotropic agents (SCN, thiocynate, CLO4; perchlorate, guanidinum ion, and the non-ionic compound urea) are ions that are poorly solvated compared to ions such as NH4+, SO42- and H2PO4-. It enhances the solubility of non-polar compounds in water by disordering the water molecules.

The water molecules disrupt the hydrophobic interactions that normally stabilize the native conformation.

The hydrophobic tails of detergents such as sodium dodecyle sulphate (SDS) also denatured proteins by penetrating the protein interior and disrupting hydrophobic interactions.

hope you all enjoy and understand 😀

thanks for reading 🙂

Anti Parallel and Parallel Beta Pleated Sheets

When i heard Mr. J.M lecture about this i was like…..

images (1)

then i was like ….????…


So here is my attempt at an ‘Idiots guide to Anti-Parallel and Parallel Beta Pleated Sheets”…!!!!


  • Beta sheets are parallel if the polypeptide strands run in the same direction, N-terminus to C-terminus. The N-terminus of one beta strand will be opposite the N-terminus of the other beta strand.
  • The parallel arrangement is less stable because the geometry of the individual amino acid molecules forces the hydrogen bonds to occur at an angle, making them longer and thus weaker.



  • Beta sheets are anti-parallel if the polypeptide strands run in opposite directions. The N-terminus of one beta strand will be opposite the C-terminus of the other beta strand.
  • In the anti-parallel arrangement the hydrogen bonds are aligned directly opposite each other, making for stronger and more stable bonds.
  • An anti-parallel beta-pleated sheet forms when a polypeptide chain sharply reverses direction. This can occur in the presence of two consecutive proline residues, which create an angled kink in the polypeptide chain and bend it back upon itself.

Hope this helps 😀


What are essential amino acids?


I remember last week that Mr. J.M bought a question on the protein quiz “What is an essential amino acid?” and the first thing that came to mind was tryptophan (click link to view), although 0.2% right that is just and example.

So we have read and heard a lot about essential amino acids and by extension essential proteins…….like really what are they?? :S


An essential amino acid cannot be synthesized by the human body and therefore we rely on our diet (meats, legumes etc, ) to get these essential amino acids.

Some examples of essential Amino Acids are :

  • Histidine
  • Isoleucine
  • Leucine
  • Lysine
  • Methionine
  • Phenylalanine
  • Threonine
  • Tryptophan
  • Valine
  • Arginine

Now since there are essential amino acids…. then there must be non- essential amino acids. ….. Correct is Right.

Non-essential amino acid is such that can be synthesized by the body.

Some examples are: 

  • Alanine
  • Asparagine
  • Aspartic acid
  • Cysteine
  • Glutamic acid
  • Glutamine
  • Glycine
  • Proline
  • Serine
  • Tyrosine


Amino Acids and Proteins

FuN fAcTs AbOuT pRoTeInS



  1. Hair is made up of a protein called keratin, which forms a helical shape. This protein has sulfur bonds, and the more sulfur links it has, the curlier a person’s hair will be. That would explain why my hair is so curly.
  2. The lifespan of most proteins totals two days or less. However, the recent discovery of extremely long-lived proteins may provide scientists with insight into cell aging and neurodegeneration
  3. The older, larger, and more mature a bean grows, the more protein it has. Mature roasted soybeans have the most protein, with 39.6 grams of protein per 100-gram serving
  4. HAHA this is too funny…realllyyy …..Proteins can have bizarre names. For example, the protein Pikachurin is a retinal protein that was named after a Pokémon character Pikachu. The protein Sonic Hedgehogwas named after Sonic the Hedgehog. A blue protein is named Ranasmurfin, after the Smurfs.
  5. Complete proteins (whole proteins) are proteins that contain all nine of the essential amino acids. Typically, proteins from animal foods such as meats, poultry, fish, dairy, and eggs are complete. Incomplete protein sources usually include nuts and vegetables.
Protein Requirements Change with Age 
Life Stage Protein Needed (in grams)
Infant 10
Teenage Boys 52
Teenage Girls 46
Adult Men 56
Adult Women 46
Pregnant/Lactating Women 71

Just making learning fun 😀


Amino Acids and Proteins Part 1

I just figured out how to use colour fonts…*hides face*

We have been studying this since ….we were in primary school and we barely scratch the surface as it is now…

In our lecture with Mr. J.M we covered the zwitterion, peptide bond and types of proteins.

Anyways … this is just a little recap about proteins …..

Amino Acids

  • Complex organic compounds that contain the elements carbon, hydrogen, oxygen, nitrogen and sometimes sulphur
  • Macromolecules with varying molecular masses ranging from thousands to million
  • There are 20 different amino acids.
  • The potential variety of the proteins is unlimited because of the sequence of amino acids is specific for that protein and determines the functions.


  • Colourless, crystalline solids
  • Soluble in water, insoluble in inorganic solvents
  • In neutral aqueous solutions they exist as dipolar ions (zwitterions) and are amphoteric possessing both acidic and basic properties.

Just a little outside info: Each amino acid has its own specific pH at which it will exist as a zwitterion.


pH is the measure of the amount of hydrogen ions in solutions. Low pH mean that the concentration of hydrogen ions is very high and vice-versa. Amino acids and by extension proteins can function as buffers or compounds which resist changes in pH. This is because amino acids, zwitterion, that is they have both positive and negative regions on the molecules. This makes it possible for them to combine with both acidic and basic substances.


In acidic conditions (low pH)

  • Lots of H+ in solution
  • If amino acids are also in the solution H+ will be picked up and bound by the negative carboxylic acid…. Effectively taking the place of the H+ ions out of the solutions therefore an increase in pH.

In basic conditions (high pH)

  • Too little of H+ in the solution
  • If the amino acids are in the solution the amino group would release their H+ into the solution…. and thus decreasing  the  pH.


Just a little outside info: Proteins are important buffers within a cell since they help to maintain the homeostatic environment for optimal functioning of enzymes and other cell reactions.

The Peptide Bond

  • Forms between two amino acids

# of Amino Residues

joined by Peptide Bond








  • A polypeptide is made of a chain of up to several thousand amino acids.
  • A protein may possess one or more polypeptide chains.
  • The covalent peptide bond that forms between amino acids can be broken bt enzyme hydrolysis or acid/alkaline hydrolysis

Just a little outside info: In nature the chain only grows on the COOH side i.e. additional amino acids can only be added to the carboxylic side.



 Taylor, D. J.. Biological science. 3rd ed. Cambridge: Cambridge University Press, 1997.  ]

Largest Amino Acid

In our biochem lecture we learnt that Glycine is the smallest amino acid

Recap: Glycine:

Glycine chemical property is that of an aliphatic -R – group and its physical property is that it is non-polar. It can be inside or outside of the protein molecule. In aqueous solution at or near neutral pH, glycine will exist predominantly as the zwitterion (click like to see zwitterion)

The isoelectric point or isoelectric pH of glycine will be centered between the pKas of the two ionizable groups, the amino group and the carboxylic acid group.

In estimating the pKa of a functional group, it is important to consider the molecule as a whole. For example, glycine is a derivative of acetic acid, and the pKa of acetic acid is well known. Alternatively, glycine could be considered a derivative of aminoethane.


Knowing this have you wondered about the largest amino acid….


Tryptophan, an essential amino acid. It belongs to an AROMATIC – R – group unlike glycine and is also non-polar. It is also a derivative of alanine, having an indole substituent on the β carbon. The indole functional group absorbs strongly in the near ultraviolet part of the spectrum.

The indole nitrogen can hydrogen bond donate, and as a result, tryptophan, or at least the nitrogen, is often in contact with solvent in folded proteins.

tryptophan                     Image

[credits: The Biochemistry Project]