Tutorial on amino acids and proteins.

Today’s tutorial was quite something that I decided that I needed to write something about it.

 

IT opened my eyes to the intensity of the course and the details that is required for doing well in the course. Specific examples and details of certain chemical reactions must be carefully noted. This is what, I believe, distinguishes an A+ student from an average, or a student looking to get a bare pass.

Let’s hope I’m that A+ student.

 

So far this course has consumed most of my time. I have been neglecting my other courses in an attempt to TRY to stay on top of biochemistry. So far, I cant exactly say that I am in fact on top of things, or at the level it seems I’m expected to be at. I’m not sure how much more of my time this course is going to consume.

 

Biochemistry is taking over my life !

Amino Acids

Hey guys 🙂

I know its been a while since I’ve posted anything ( a week to be exact ) but ive been quite the busy bee! So that being said I decided to give a major post on the basics for amino acids 🙂

So let’s start off with the basic stuff.

question

and Last but NOT least:

question

What are amino acids?

Let’s start with a basic structure :

Reference: http://www.ucl.ac.uk/~sjjgsca/ProteinStructure.html

So there we have it folks! the basic structure of an amino acid, containing an amino group, a carboxyl group, and a variable R group also known as the “side chain.” Later on we will see that the interactions between the varying side chains, as well as the amino group play an important role in forming different types of bonds for various structures.

Two amino acids, come together, through condensation, to form a peptide bond.

Peptide bond

Reference: https://courses.worldcampus.psu.edu/welcome/biol011/lesson02_09.html

Later on in this blog, we will refer back to peptide linkages, and polypeptide chains, so make sure you understand the basics!!

Moving on we ask;What are amino acids used for?

Well to begin with, there are two different types of amino acids, Essential, and non essential amino acids. Naturally I am sure you will be able to guess the difference between two.

Essential amino acids :

These amino acids ust be obtained from the diet, since they cannot be synthesised on their own. There are roughly ten essential amino acids.

Non-Essential amino acids:

The body is able to synthesize these amino acids. Usually the body uses already exsisting carbon skeletons, and convert them to the respective amino acids. One example of this is the conversion of alanine to pyruvic acid.

Here’s a general picture of whats happening for the curious ones:

c01f010

Reference: https://kubon-sagner.e-bookshelf.de/products/reading-epub/product-id/595941/title/Essential%2BBiochemistry%2Bfor%2BMedicine.html?autr=%22Mitchell+Fry%22

Finally we move on to some chemical reactions involved with amino acids! 😀

Here’s a look at general peptide chain:

peptide1

Reference:http://www.ucl.ac.uk/~sjjgsca/ProteinStructure.html

From these peptide bonds, polypeptide chains can be formed,which can cause further structures to be created, as the polypeptide chain begins to fold. The polypeptide chain folds as a  result of different interactions between the different amino acids and the formation of hydrogen bonds, sometimes various sulphide bonds The different degrees of folding in the structure, classifies it as either primary,secondary or tertiary.

Primary and Secondary structures.

Reference: http://www.mhhe.com/biosci/ap/ap_prep/chemH5.html

Let’s Pause for a cause here and get some definitions under our belt.

Here’s a useful website I found describing everything in a pretty concise understandable manner.

http://www.mhhe.com/biosci/ap/ap_prep/chemH5.html

They give a concise definition of amino acids stating that they are a  “Class of organic acids that comprise the building blocks for proteins.”

They also explain hydrogen bonding in an easy, understandable way stating that hydrogen bonds are, ”  A weak attraction between a slightly positive hydrogen atom on one molecule and a slightly negative oxygen or nitrogen atom on another molecule, or between such atoms on different parts of the same molecule; responsible for the cohesion of water and the coiling of protein and DNA molecules, for example.”

Understanding hydrogen bonds is important seeing as they form the basis for primary, and therefore secondary and tertiary structures.

So now that we’ve taken a moment to understand, let’s dive straight into these amazing structures 😀

Primary structures:

  •  These are a linear sequence of amino acids joined by peptide bonds
  • The nucleotide bases in the gene encoding the protein determines this sequence.

Secondary structures:

  • Regular folding of regions in polypeptide chains are observed.
  • Two examples of secondary protein structures can be seen in the alpha helix and beta pleated sheet.

Tertiary Structures:

  • These are usually globular
  • For soluble globular proteins, they are usually folded in away that the hydrophobic links are buried within the structure, while the hydrophilic chains are on the outside.

protein-structure

Reference : http://www.umass.edu/molvis/workshop/prot1234.htm

So there you have it folks! 🙂 the basics of amino acids.

Hope you had a fun time learning 😀

Next time we’ll go into detail about the secondary structures of proteins, that is, alpha helices and beta pleated sheets.

Until next time

Au Revoir

Carbohydrates Part 2

Hey folks, its time for the continuation of my last post on carbohydrates. In fact personally it’s the icky part of biochemistry for me, the chemistry part.

OH. THE.HORROR.

OH. THE.HORROR.

Here’s a simple video, that gets straight down to the point which I found to be quite helpful 🙂

It’s divided into three parts :


Carbohydrates !!

Carbohydrates.

A pretty big topic to cover if you ask me. One post alone cannot cover the vast amount of information presented to a meek uni student as myself. But we must start somewhere.

34352507

Previously I had constructed a worlde, with various key words which played an important role, or that were subtopics of the subject of carbohydrates under biochemistry.

Let’s start somewhere shall we?

First of all, what exactly are carbohydrates?

Carbohydrates, simply put are hydrates of carbon : (CH2O)n. They also provide energy, and are the most abundant molecule in our chemistry world as we know it.

PAUSE.

Let’s put all of this carbohydrate talk into our daily lives to get some perspective :

tumblr_m0tw42lmjV1qeow5po1_500 (1)

YES !! that’s right. Bread is a form of carbohydrate, or “carbs” as we refer to them as.

Fun fact: Cakes cookies and beer are empty carbs or calories, providing no nutrition value at all.

What are the functions of carbohydrates?

one may ask. Since we are both exploring the world of biochemistry together, id be more than happy to help 🙂

Functions include:

1)Storage

2)Formation of precursor molecules

3)Playing a structural Role

4) Acting as an energy source.

These functions are pretty self-explanatory but still important points to note when learning about carbohydrates.

Preview

The Wonders of the Cell

This past week, the cell was re-introduced to the eager students of biochem 1362. I say reintroduce since this topic was previously covered for our secondary school exams. The cell had always been a favorite topic of mine, since the first topic I ever learnt as a young student, for science, was in fact the cell.  While we did go into some further detail about the cell, most of the knowledge required to be learnt was previously taught and understood.

With that being said however, I must admit that I was in fact a bit rusty on the entire topic.

animal-cell                                                   plant-cell prokaryotic-cell

( pictures found at: http://www.s-cool.co.uk/a-level/biology/cells-and-organelles/revise-it/introduction-to-cells)

For example, my mind had completely blanked upon the endosymbiosis theory of evolution. This theory, in simple man terms, states eukaryotic cells were originated from prokaryotic cells. To support this theory there were several points of evidence. My mind, of course, was completely blank on this, so I referred to :  http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter4/animation_-_endosymbiosis.html for help.

After viewing the video I was able to recall that the six points of evidence supporting the theory included:

1. Mitochondria and chloroplasts are the same size as prokaryotic cells, divide by binary fission.

2. Mitochondria and chloroplasts have their own DNA that is circular, not linear.

3. Mitochondria and chloroplasts have their own ribosomes, 70s.

4. Mitochondria are of similar size to bacteria and are surrounded by two membranes.