Reflection VII: AMINO ACIDS & PROTEINS P2!!!

Amino Acids form undergo a condensation reaction to form a dipeptide.

Formation of Peptide Bond

This dipeptide can remain or link with more amino acids to form a polypeptide.

Polypeptide Chain

-The unique sequence of amino acids in the  polypeptide chain give rise to unique proteins that code for many things such as hair, skin, nails and enzymes.

Structure-Function Relationship

-Polypeptides must be folded to be functional proteins.

-Protein structure dictates protein function.

-Proteins have four levels of structure.

• Primary Structure
• Secondary Structure
• Tertiary Structure
• Quaternary Structure

Primary Structure.

-This the sequence of amino acid units, and comprises the protein’s overall biomolecular structure.

Primary Protein Structure

Secondary Structure 

This is the specific geometric shape caused by intramolecular and intermolecular hydrogen bonding of amide groups. Consists of two types alpha helix and beta pleated sheet.

Secondary Structure of Proteins

Tertiary Structure

This is the final specific geometric shape that a protein assumes. This is determined by a variety of bonding interactions between the “side chains” on the amino acids. These bonding interactions may be stronger than the hydrogen bonds between amide groups holding the helical structure. As a result, bonding interactions between “side chains” may cause a number of folds, bends, and loops in the protein chain. Different fragments of the same chain may become bonded together.

There are four types of bonding interactions:

1. Disulfide bonds are formed by oxidation of the sulfhydryl groups on cysteine. Different protein chains or loops within a single chain are held together by the strong covalent disulfide bonds.
2. Hydrogen bonding between “side chains” occurs in a variety of circumstances. The most usual cases are between two alcohols, an alcohol and an acid, two acids, or an alcohol and an amine or amide.
3. Salt bridges/ Ionic bonds result from the neutralization of an acid and amine on side chains. The final interaction is ionic between the positive ammonium group and the negative acid group. Any combination of the various acidic or amine amino acid side chains will have this effect.

4.  Non-Polar Hydrophobic Interactions: are believed to contribute significantly to the stabilizing of the tertiary structures in proteins. This interaction is really just an application of the solubility rule that “likes dissolve likes”. The non-polar groups mutually repel water and other polar groups and results in a net attraction of the non-polar groups for each other.

The four types of bonding that takes place within a protein’s tertiary structure that give it it’s geometrical shape.

Quaternary Structure

This involves the clustering of several individual peptide or protein chains into a final specific shape. A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains into a particular geometry.

Quaternary Structure of Haemoglobin

There are two major categories of proteins with Quaternary structure:.

1. Fibrous Proteins: the result of the interaction of many individual protein chains. Some are composed of hydrogen bonding on amide groups on different chains is the basis of beta-pleated sheet as seen in silk proteins.While other fibrous proteins such as keratins  are composed of coiled alpha helical protein chains with other various coils analogous to those found in a rope.  Fibrous proteins are insoluble, and play a structural or supportive role in the body, and are also involved in movement (as in muscle and ciliary proteins).
2. Globular Proteins:  globular proteins fold back on themselves to produce compact, nearly spherical shapes. Most globular proteins are water soluble and hence are relatively mobile within a cell. Some examples are enzymes, antibodies, hormones, toxins, and substances such as hemoglobin.

Fibrous and Globular Proteins

Well that’s all I can remember; time to re-watch the lectures 😛

Good luck my fellow Biochemians

Amino Acids & Proteins: Le Multiple Choice Question Time :D

Alrighty guys its time for some lightning rounds! Time to see how much we’ve learnt / need to learn on amino acids and proteins. It’s easy I promise 🙂

Please select the letter corresponding to the answer you think is right and based on the question asked. Please place your answer in the doobly doo below (comment section) and feedback on your answers or any queries will be given.

If you’re not sure you’re ready just go through some of my previous posts or your own notes and come back and try.

Here we go.

1. In amino acids (with the exception of glycine) the ‘alpha’ carbon is:

A. The carbon found in the centre of the structure.

B. An isotope of carbon contained in the amino acid.

C. The chiral centre of the amino acid.

D. The carbon bonded to the amino group, the carboxylic group, hydrogen and a substituent R group.

E. The carbonyl carbon.

____________________________________________________________________________________________________

2. A Cystine molecule is formed via:

A. The oxidation of two cysteine molecules

B. The formation of a peptide bond between two cysteine molecules

C. The reduction of two cysteine molecules

D. The formation of a disulfide linkage via oxidation of two cysteine molecules

E. The condensation reaction between two cysteine molecules

_______________________________________________________________________________________________________

3. The main classes of amino acids are:

A. Non-polar, Polar, Acidic, Basic

B. Aromatic, Non-Aromatic, Polar, Non-Polar, Basic, Acidic

C. Acidic, Basic, Hydrophobic, Polar, Non Polar

D. Simple, Complex

E. Acidic, Basic, Polar, Non-Polar, Aromatic

_______________________________________________________________________________________________________

4. Which level of protein structure determines how it folds into its unique three dimensional structure, hence in turn determines the function of the protein?

A. Primary

B. Secondary

C. Tertiary

D. Quaternary

E. All of the above

_______________________________________________________________________________________________________

5. Which statement is false?

A. the arrangement of protein subunits (polypeptide chains) in 3-d complexes constitutes to quaternary structure.

B. globular proteins consist of polypeptide chains folded into spherical or globular shapes.

C. fibrous proteins usually consist of chains with multiple type secondary structure.

D. fibrous proteins consist of polypeptide chains arranged in long strands or sheets.

E. fibrous and globular proteins differ functionally.

Thank you for completing my MCQs 😀

Amino Acids & Proteins Wordle

Hey guys!!

After reviewing Amino Acids and Proteins I decided to make a wordle of some of the key words related to the topic. Enjoy 😀

Reflection VI: AMINO ACIDS & PROTEINS P1!!!

You might have guessed from the title that we have moved on in classes to proteins and amino acids.

One could say we’re almost done. As we’re getting a quiz soon So let’s prepare shall we?

Proteins are made up of many Amino Acids.

They have the general structure of four groups attached to an alpha carbon

• amino
• carboxyl
• hydrogen
• R group

Source: http://www.whitetigernaturalmedicine.com/wp-content/uploads/2012/02/amino-acid-structure.jpg

– There are 20 common amino acids found in the body.

-They are divided in to 3 groups

• Polar Amino Acids (Hydophillic)

• serine
• threonine
• cysteine
• tyrosine
• asparagine
• glutamine

• Non-Polar Amino Acids (Hydrophobic)

• glycine
• alanine
• valine
• leucine
• isoleucine
• methionine
• phenylalanine
• tryptophan
• proline

• Charged Amino Acids
• • aspartic acid (acidic, negative charge)
  • glutamic acid (acidic, negative charge)
  • lysine (basic, positive charge)
  • arginine (basic, positive charge)
  • histidine (basic, positive charge)

20 Common Amino Acids in the human body Orange: Non – Polar (hydrophobic) Green: Polar (hydrophillic) Pink: Charged – Acidic Blue: Charged – Basic

Reflection V: Video Discussion Anyone?

AMINO ACIDS AND PROTEINS P1

This video done by my Hokage-sema himself, begins discussing the common overall structure of amino acids and how they differ due to constituent R groups, leading to formation of many different  types and different classes of amino acids. He goes onto explain and classify the 20 standard amino acids into polar, non-polar, aromatic, positively charged (acidic) and negatively charged (basic) groups explaining how the R groups contribute to classification.

This video then goes on to clear up the (confusing at first because of the names) formation of Cystine, via oxidation, from two Cysteine molecules. This is extremely beneficial to know because this dipeptide (Cystine) is not formed via normal peptide bond formation. A disulfide linkage is made between the two molecules which is a VERY STRONG LINKAGE (in the world of protein linkage). Don’t believe me? Check out the video. Hokage-sema does not lie.

Moving on, the zwitterionic form of amino acids are discussed, followed by the classification of amino acids yet again, into essential (required to be taken in via the diet) and non-essential (synthesised by the body) amino acids.

This video also aids greatly before laboratory exercises. Two tests were discussed. The Ninhydrin test is also touched on; this a test performed to detect the presence of amino acids(which are colorless) from a solution. If amino acids are present a purple color is observed.  Another test brought forward is the Biuret test. This test is performed to detect the presence of proteins (no not amino acids, PROTEINS). If proteins are present, a purple color is formed (yet again).

The formation of peptide bonds is also covered in this video (whoo moving so fast). From this I can say the concept is very clear, a condensation reaction occurs between the amino group of one amino acid and the carboxylic group of another, hence forming a covalent peptide linkage. I’ll post something up to make it clearer (or you can just check out the vid?). This then leads into the formation of greater complexes of amino acids, the dipeptides, the polypeptides and of course proteins.

Lastly the functional classes of proteins are touched on, which include acting as receptors, forming channels, acting as transporters, storage, enzymes, structural roles and aiding in immune response. Want examples? Check out the vid!!

Well I won’t spoil the ending of the video for you guys because I’m sure you want to check out that video yourself. 😀

How bout we watch part 2 together?

Reflection IV : Moving On

Hey guys! We’re in week 4 now, and about a quarter way into the semester 😀 Time is just flying by. Hope you guys had a safe and enjoyable Carnival  and are getting back into some work.  Anyways time for some biochem adventures.

To Adventures

This week in biochemistry we  pressed on with amino acids. To be honest amino acids is one of my favourite topics because like carbohydrates, the molecular biology is quite simple once the basics are understood.

Amino acids are quite important to us, did you know

Thinking along these lines I guess you can say amino acids are like the lego blocks of life.

Today in class we went over the basic structure of amino acids and went into detail about how the nature of the amino acid or the type of amino acid is determined by the R Group attached to the alpha carbon.  We also went into the touched on the 20 essential amino acids and how they can be classed according to traits determined by their R group. Here’s a picture to get the idea

The 20 Essential Amino Acids Categorized

Welp, thats all for now guys.

Happy studies 😛