Garage Sale?

I have recently been aspiring to only own things that I need and not want. After a lot of getting rid of things to the church and friends I decided to start accumulating it.

I am still finding things I don’t need hidden away like the possession orientated person I was. So I have decided to sell it. Yet another garage sale. I don’t know why but gumtree and eBay just don’t work for me.
So here goes nothing! I want to get rid of everything by 10am today…

Enzymes and Co-Enzymes

Wow! I cant believe I made it to post 300. Back to chemistry notes again, sorry but its really basic so it should make sense I hope, my handwriting is illegible sometimes so trying to type it up is always not fun. Check out General, Organic and Biological Chemistry by K.C Timberlake, that’s where the majority of my notes come from.


Enzymes and Co-Enzymes

Nature of Enzymes as Catalysts

Enzymes are proteins. They catalyse (Speed Up) most chemical reactions taking place in cells.

The increase the rate of reaction by lowering the amount of energy needed. They also have a unique 3D shape that fits reactants. Enzymes don’t affect the equilibrium as it increases the speed of both forward and reverse reactions.

Enzymes may recognise and catalyse:

  •  Absolute (1 substrate)
  • Group (A group of similar substrates)
  • Linkage (A certain type of bond )


  • Catalyse the same reaction in different places in the body
  • Can be used to identify the organ or tissue involved in damage or disease

Diagnostic Enzymes

  • The levels of diagnostic enzymes determine the amount of damage done in the tissue.
  • For example, to look at pancreatic disease, there would be higher levels of Amylase and cholinesterase lipase

System of Classifying Enzymes

The name of an enzyme is their identification, they mainly end in –ase. The name categorizes them by the reacting substance – sucrose for sucrose. The name also describes the function: oxidase = oxidation. But it can be a common name for example the digestive enzymes.

Class Reaction Catalysed
Oxidoreductases Oxidation Reduction
Transferases Transfer group of atom hydrolysis
Hydrolases Hydrolysis
Lyases Add/Remove atms to/from a double bond
Isomerases Rearrange atoms
Ligases Use ATP to combine molecules

This table is from Timberlake, Pearson Education


Enzymes and Substrate Interactions

Active Site:

  • A place in an enzyme that fits the shape of the molecule (Substrate)
  • Contains Amino Acid R groups that align and bind the substrate to it.
  • Releases product when the reaction is complete

Lock and Key Model:

  • The active site has a rigid shape (Lock)
  • Only a substrate with a matching shape will fit (Key)

Lock and Key fit is an Enzyme(E)-Substrate(S), the ES complex

  • E+S= ES
  • ES = E+P (Product)
  • The Substrate is converted to Product, the product is released from active site when it is no longer attracted to it.

Induced Fit Model:

  • Active site is flexible
  • The active site and substrate move to fit with each other
  • Has a bigger range of substrate specificity


Enzyme Activation and Inhibition

Enzyme and Substrate Concentration:

  • The enzyme, substrate and the environment all play a role in the Enzyme activity.
  • As the rate of enzyme concentration increases, so does the rate of reaction. More substrate binds with enzymes.
  • As the rate of substrate concentration increases, so does the rate of reaction. When the enzyme is saturates, maximum activity occurs.

Enzyme Action:

  • Temperature affects enzymes, most are active at 37 Degrees Celsius  (regular body temp), at lower temperatures, Enzymes lower in activity (like they go to sleep) but can recover as they return to their optimum temperature. At higher temperatures above optimum , the enzyme will denature and no longer be useful.
  • The same applies with pH levels, most enzymes are most active at 7.4pH (regular body pH). They lose activity at higher and lover pH and denature as they can no longer function in their environment. But in different parts of the body the optimum pH can be higher or lower.

Inhibitors: can prevent substrates from fitting into the active site or can cause a lesser catalyst effect. For example: Enzyme + Substrate = ES = Enzyme + Product, with an inhibitor: Enzyme + Inhibitor = EI = No product.

Enzyme Regulation

Rate of reaction that controls the amount of product  is controlled by Zymogens and Allosteric Enzymes.

Zymogens (pro-enzymes):

  • Are inactive enzymes
  • Activated when a peptide is removed
  • Proteases are in zymogen form
  • Digestive Enzymes: are produced as zymogens in a organ and transported to another when they are needed.

Allosteric Enzymes:

  • Is an active enzyme that is solely protein
  • A positive regulator: increases the binding of substrate and enzyme = makes the rate of reaction faster.
  • A negative regulator: stops the binding of substrate and enzyme = slows the rate of reaction.

Enzyme Cofactors

  • A simple enzyme is active and a protein
  • Lots of enzymes are only active when they combine with a cofactor (metal ions or small molecules)
  • COENZYME = cofactor that is a small organic molecule
  • A coenzyme prepares the active site for catalyst

Book Club

I feel like I am lacking the drive to finish books because I feel a huge loss each time I finish one.

To people who don’t enjoy reading books it may give the impression of being shallow and narrow minded.

But in fact books are a gateway to broaden ones perspective .


So I am going to aim to finish reading a book every two week as we all have life and commitments getting in the world. Then I hope that I will be able to write a post on it and get feedback from anyone else who chooses to read it with me.

I forgot I loved to read. I hope that it never happens to you.


Originally the stating book I wanted was Mansfield Park, I know its an old book which many people had to read for school and not pleasure. BUT I want to read it, it has been sitting on my shelf since I read emma and pride and prejudice for A levels so it needs to be read.
…. But I can’t seem to find it and my libraries copy is lost so it is now along to :

Will be Pride and Prejudice and Zombies… All these books your library should have.

NOW! Give me some feedback so we can move away from the Jane Austen and look at some new books or you will be forced to endure the 47 books in a pile in my room waiting to be read.

Proteins, The Structure and Function, An Introduction

Hi everyone, this is a shorter post about a glance at proteins – most of the information came from my notes and Timberlake’s book which is referenced down the bottom.

Structure and Function Of Proteins

Proteins are made up for 20 different amino acids, all arranged in different sequences. This determines the characteristics and functions. Proteins function as Enzymes, Hormones and are important for structure, transport, protection, storage and muscle contraction.

Types of Proteins

Structural Level Characteristics
Primary Peptide bonds join amino acids in a specific sequence in a polypeptide
Secondary The alpha helix, and beta pleated sheet, or triple helix forms by hydrogen bonding between the atoms in the peptide bond along the chain
Tertiary A polypeptide folds into a 3D shape stabilized by interactions between R groups to form a biologically active protein
Quaternary 2 or more protein subunits combine to form a biologically active protein

This table is from Pearson Education in the reference.

Formation of a Peptide Bond

As we discussed in Function and Structure of Amino Acids, a peptide bond is an Amide Bond between the carboxylic group of one amino acid and the next amino acid group

Primary, Secondary, Tertiary and Quaternary Structures of Proteins

The Primary Structure of a Protein is:

  • the particular sequence of amino acids
  • the backbone of a peptide chain or protein

The nonapeptides (9 amino acids) oxytocin (induces labour) and vasopressin (antidiuretic hormone):

  • Have similar primary structures
  • Differ only in the amino acids at positions 3 and 8


  • First protein to have its structure determined
  • Has a primary structure of two polypeptide chains linked by disulphide bonds.

Has a chain A with 21 amino acids and a chain B with 30 amino acids

The Secondary Structure

The secondary structure of a protein indicates the 3D spatial arrangements of the polypeptide.

An Alpha Helix:

  • has a coiled shape held in place by the hydrogen bonds between the amide groups and the carbonyl groups of the amino acids along the chain.
  • The hydrogen bonds between the H of a –N-H group and the O of C=O of the fourth amino acid down the chain.

A Beta Pleated Sheet:

  • Consists of polypeptide chains arranged side by side
  • Has hydrogen bonds between chains
  • Has R groups above and bellow the sheet
  • Is a typical of fibrous proteins such as silk

A Triple Helix:

  • Consists  of three alpha helix chains woven together
  • Contains large amounts of glycine, proline, hydroxy proline, and hydroxyzine that contain –OH groups for hydrogen bonding
  • Is found in collagen, connective tissue, skin, tendons and cartilage

Tertiary Structure

The interactions of the R side group give a protein it’s specific 3D tertiary structure. The side groups only interact in Tertiary Structures.

Globular Proteins:

  • Have compact, spherical shapes (Globe – globular like the world)
  • Carry out Synthesis, Transport and metabolism in the cells
  • Such as myoglobin store and transport oxygen in muscle

Fibrous Proteins:

  • Consists of long, fiber-like shapes
  • Such as alpha keratins make up hair, wool, nails and skin

Quaternary Structure

This is the combination of two or more tertiary units. It is stabilized by the same interactions found in tertiary structures. The Quaternary Structure of Hemoglobin consists of 2 alpha chains and 2 Beta chains. The heme group in each subunit picks up oxygen (Oxygen binds at Heme group) for transport in the blood to the tissues. This occurs in Proteins with more than one chain.


Duration of Hydrolysis of Proteins

Protein Hydrolysis is essentially  the chemical reaction where you break the peptide bond – but it needs enzymes. It “splits the peptide bond to give smaller peptides and amino acids” (Timberlake ). Hydrolysis happens in digestion of proteins (by digestive enzymes). Hydrolysis happens when amino acids are needed to synthesise new proteins or repair tissues.

Types of Agents that Denature Proteins

Denaturing is when a disruption of bonds in secondary, tertiary and quaternary protein structure occurs…. A bit like “death”

  • Heat– like when you cook eggs – the egg white solidifies and you cant reverse > this is what happens when organic compounds break apart hydrogen bonds and disrupt hydrophobic interactions.
  • Acids and Bases –like when you poach an egg in vinegar. Egg + Vinegar = Acid
  • Reducing agents – like a hair perm
  • Detergent – disrupt hydrophobic interaction causing protein chains to unfold.

Heat –this is why kids cant/shouldn’t have a temperature higher than 39degrees Celsius or death will follow as vital enzymes denature. Adults cant/shouldn’t go past 40 degrees Celsius or death will follow.


Timberlake, KC 2007, General, Organic and Biological Chemistry, 4th Edition, Pearson, USA

Structure and Function of Amino Acids Introduction

Hi guys and gals, this is a summary of my notes on Amino Acids, it should give you a run down on the basics and skip over any of the stuff you dont REALLY Need to know to have a vague understanding.  If this isnt really to your taste let me know. 🙂 

 Amino Acid

Proteins are composed of 20 different amino acids, in each protein the amino acids are arranged in a specific sequence that determines the characteristics and the function within the body of the protein.

Essential Amino Acids

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

Complete proteins, such as eggs, milk, fish and meat contain all of the essential amino acids. Plants, Grains, beans and nuts are deficient in one or more essential amino acid. The MUST be obtained from the diet, as there are 10 amino acids not synthesised by the body. A complete protein will contain all 10. By combining legumes and grains a complete protein is made as each missed what the other has.

Protein = Macromolecule that contains: Carbon, Hydrogen, Oxygen and Nitrogen: all needed by the body for growth, repair and to make up enzymes: a polymer made of amino acids

Food Source Amino Acid Missing
Egg, Milk, Fish, Meat and Poultry NONE
Wheat, Rice and Oats Lysine
Corn Lysine and Tryptophan
Beans Methionine and Tryptophan
Peas Methionine
Almonds and Walnuts Lysine and Tryptophan
Soy Low in Methionine


Classification of a Protein according to its Class and Function

Structure Determines Function.

Class Function Examples
Structural Provides structural components Collagen in tendons and cartilage
Contractile Makes muscles move Myosin and actin – contract muscle fibers
Transport Carry essential substances around body Hemoglobin takes oxygen around the body
Storage Able to store nutrients Casein stores the protein in milk
Hormonal Regulates metabolism and  the nervous system Insulin regulates blood glucose levels
Enzyme Catalyse biochemical reactions in the cell Sucrase catalyse the hydrolysis of sucrose
Protection Recognise and destroy foreign substances Immunoglobin stimulates the immune response


General Structure of Amino Acids

Amino Acids are the building blocks of proteins

  • They contain a Carboxylic Acid group and an amino group on the Alfa Carbon
  • They are ionized in a solution  – undergo an internal based reaction
  • Each contain a different side group (R)
  • Amino, Carboxylic, Hydrogen and Carbon: R side chain is dissolvable in aqueous solution

Types of Amino Acids

  • Non Polar (Has no PH) (Hydrophobic) – Hydrocarbon side chains CH3
  • Polar (Hydrophilic) –Polar or Ionic side chains CH2 – OH
  • Acidic (soluble in water) (Hydrophilic) with an acidic side chain
    C –O-
    =O (acids in aqueous solutions release hydrogen)
  • Basic (soluble in water)(Hydrophillic) with NH2 side chains
  • Sulphur containing



Non Polar Amino Acids

  • Has an R group that is H, an Alkyl group or aromatic (H can be replaced by a benzein ring sometimes)

Polar Amino Acids

  • Has an R group that is an alcohol, Thiol or amide (up to five amides are water soluble)

Acidic and Basic Amino Acids

  • An amino acid is acidic with a carboxylic R group COO-
  • An amino acid is basic with an amino R group NH3+

Fischer Projections of Amino Acids

  • Amino Acids are chiral except for glycine
  • Amino Acids have Fischer Projections that are stereoisomers
  • Amino Acids that are L are used in Protiens (Mostly L acids are what the body uses)

Amino Acids and Zwitterion

A Zwitterion

  • Has charged –NH3+  and COO- Groups
  • Forms when both –NH2+  and –COOH groups in an amino acid ionize in water
  • Has equal + and – charges at the isoelectric point (pl)

Buffering Abilities of Amino Acids

Release or accept of hydrogen ion. In solutions more basic than pl, the -NH3+ in the amino acid donates a proton. And in solution more acidic than the pl, The COO- in the amino acid accepts a proton.

As Acids = release hydrogen in water environments.

As Base = accept hydrogen in acidic solution.


The properties of Amino Acid – Cysteine

The amino acid, Cysteine, contains sulphur – eg Hair.


A peptide bond is an amide bond, formed between a carboxylic group of one amino acid and the amino group of the next amino acid.

Peptide refers to Protein; short protein, up to 50 amino acids. Polypeptides are much larger.

Dipeptide Formation: two amino acids link to peptide . During Synthesis water is removed : called Dehydration Synthesis.


Electrophoresis : Separation of Amino Acids

In electrophoresis an electrical current is used to separate the mixture of amino acids.

  • Positively charged amino acids move towards the negative  electrode.
  • Negatively charged amino acids move towards the positive electrode.
  • An amino acid at pl does not move
  • The amino acids are identified as separate bands on the filter paper