Enzymes

Introduction

Our focus this week was on a particular group of proteins called enzymes.

Enzymes are "biological catalysts", as they affect the rate of chemical reactions, thus catalysing them. They are called "biological" because they are organic, i.e. made up of carbon compounds, (proteins).

We learnt how enzymes are globular proteins, and because of their amino acid composition, (depending on DNA), how their structure affects their shape, which in turn affects their function. This means that enzymes are SPECIFIC, i.e. they can only catalyse one type of reaction.

They form particular indentations which form active sites for substrate (reactant) molecules, so changing one amino acid in the chain could affect the protein's structure, and how the different parts of the chain are bonded together. This may affect the shape of the active site, so the substrate may fit improperly, or not at all within, so the function of the enzyme is lost.

Enzymes can catalyse two types of reaction:

• ANABOLIC REACTIONS: These are involved in the building up of molecules, such as in Photosynthesis, starch is made from molecules of alpha-glucose built up together.


• CATABOLIC REACTIONS: These regard breaking down molecules, i.e. in digestion, long chains of carbohydrates are broken down to glucose, which can be absorbed, or in respiration, glucose and oxygen molecules are broken down, (then built up to make carbon dioxide and water).

All reactions and processes in your body require enzymes, and an organism's metabolism is made up of thousands of types of these enzyme reactions. Otherwise, the reactions occuring naturally would happen too slowly, and we wouldn't be able to survive. =(

RATES OF REACTION

Definition: The change in concentration of a reactant or product per unit time.

This basically means how quickly the reactants can be turned into products. Reactants need to collide successfully, reaching or surpassing the activation energy for this to happen.

To increase the rate of a reaction, you need to increase the number of successful collisions per unit time.

Factors which affect the rate of a reaction are:

• Temperature (increasing temperature increases the rate, up until a point if enzymes are involved. This is because the particles are given more thermal energy, which is transferred to their kinetic energy. Collisions are more frequent and with more energy, reaching the activation energy).


• Concentration of reactants (if there are more reactants in the same volume, more can collide with each other to form products, so increasing concentration increases reactivity rates).


• Surface area of reactants (When there is more surface area available, collisions can take place over more space, and more can happen at the same time, as reactants can contact each other more often. Increasing surface area increases the rate of a reaction).


• Use of a catalyst (i.e. Enzymes. See below for more detail on how this happens).

Enzymes affect the rates of chemical reactions, usually speeding them up. However, it is worth noting that because they are biological catalysts, they can be denatured. A reaction rate will increase as temperature increases, due to particle kinetic energy making the enzyme and substrate collide more often, but after a certain temperature, (the optimum temperature, (which they work best at), which varies for different enzymes. In the human body this is around 37 °C ), there is enough energy to overcome the different types of bonding in the enzyme, and the bonds break. This changes the shape of the enzyme, so the active site is no longer complementary to the substrate, and the reaction slows down. The enzymes can no longer perform their function because their shape unravels.

[[Denaturing is a permanent process. Additionally, pH affects how the bonds are held together, so enzymes only work at a certain range of pHs, or they denature as well.]]

ACTIVATION ENERGY

As I have mentioned above, the reactants must collide with enough energy to form a successful collision.

The ACTIVATION ENERGY: is the minimum amount of energy required to get substrates to react.

Enzymes lower the activation energy, which means that more reactant particles collide with sufficient energy to form a successful collision, and therefore, a product.
At any given temperature, higher activation energies mean slower reactions, and the lower the activation energy of a reaction, the more successful collisions occur per unit time.

It is worth taking note that the enzymes do not affect the starting energy or ending energy of a substrate or a product. It remains the same. Only activation energy changes.

Exothermic reactions are ones that give out energy (so the product energy is lower than the reactant energy).

Endothermic reactions take in energy during the reaction (so the product energy is higher than the reactant energy).

How does the enzyme increase the rate of an anabolic reaction?

It lowers activation energy, and makes it more likely the substrates will collide at a particular orientation (i.e. place). This makes it more likely they will meet, by holding them firmly in place, and form products due to a successful collision.

The Lock and Key Model

Scientists like to model their observations by comparing them to things that already exist, so they are easier to understand. The enzyme-substrate complex is compared to a lock and key.

The enzyme is thought of as a lock, with it's active site, and the substrate is the key. The complex is complementary, i.e. when joined, they complete each other.

The shape of the substrate fits perfectly into the active site of the enzyme, and they make one unit. The active site of the enzyme is like the keyhole, in which only one type of key (substrate) will operate the lock. They enzyme/lock is specific to a substrate/key to have a successful reaction/open a secret box.

The R groups in the active site of various amino acids bond to the substrate to hold them in place, but this is only temporary, until the other substrate comes along. Then the R groups return to normal on the active site, so the enzyme remains chemically unchanged, and therefore, can be used again. They are not used up in a reaction.

This means that in small quantities, enzymes are effective.

Mr Dawson tried to model this with your friend as an enzyme, a boy you like and you as substrates, and a crush concept which was amusing, but may help understanding more than this entry.

Also, we attempted to do an experiment on the effect of temperature on enzyme catalysed reactions, by using water baths at different temperatures and adding diastase (an enzyme that breaks down starch), and starch together, and then using iodine solution on spotting tiles, adding a drop after every minute.

What should have happened was that the spotting tiles would gradually reduce in blue-blackness because the starch was broken down, and this would get faster from 20-30 degrees, but then slower from 40 degrees onwards, because the enzyme would have denatured and the rate of reactions would then be slower. The experiment was unsuccessful and we abandoned it.

I think it may have something to do with the starch being too concentrated.

Then we missed Thursday's lesson because of the Maths challenge.

I hope this entry was useful. I know I've rambled on a bit, so sorry =)

Reshma xxx

What We've Learnt So Far:

What we've learnt this week in biology: (13/10/08 - 17/10/08)

This week we have been learning all about proteins, in particular a group of proteins called amino acids.

Every amino acid has a central carbon atom with four different chemical groups attatched to this atom, they are:

• The amine group (-NH2)
• A carboxyl group (-COOH)
• A hydrogen atom (-H)
• And an R group which is different for each different enzyme.

In addition to learning about the structure of an amino acid, we have been learning about the structure of proteins and the formation of bonds.

Peptide bonds - Amino acid monomers combine to form a dipeptide in a condensation reaction. The water released is made by the -OH from a carboxyl group combining with a H from the amine group of a different amino acid. The bond formed between the two different amino acids is called a peptide bond.

Ionic bonds - these are the bonds formed between charged R groups (in aqueous solutions). The negativley charged carboxyl group bonds with the posotivley charged amine group.

Disulphide bonds - this only occurs between the sulphyl group of two cysteine amino acids. There are two types of disulphide bonds: interchain which is between two different polypeptide chains and intrachain between two of the same polypeptide chains.

Hydrogen bonds - Will form between NH groups and O=C groups due to the unequal sharing of electrons, however, can also be between OH groups and O=C groups on the R groups of nearby amino acids.

Finally, the structures of protein:

• Primary structure - Amino acid monomers join together to form polypeptides. The sequence of amino acids in a polypetide chain forms the primary structure of any protein. Proteins can be made of a single polypeptide chain but are mainly made up of a number of polypetide cains. The sequence is specific for each protein.
• Secondary structure - The posotive charge of the -NH and negative charge of the -O=C on either side of the peptide bond slightly attract each other. This causes the polypetide chain to twist forming an alpha helix. Beta sheets can also be formed.
• Tertiary structure - The polypeptide chain folding to form a 3-D shape. This shape can be determined by 1. hydrophyllic amino acids sheilding hydrophobic amino acids in aqueous solution. 2. hydrgen bonds. 3. ionic bonds. 4. disulphide bonds.
• Quaternary structures - A combination of two or more polypeptide chains. The chains are held together by hydrogen bonds, ionic bonds and interchain disulphide bonds.

Hope this is useful and sorry for all of the spelling mistakes!

Christina xx

Common Assessment One Test

One way in which I would like you to use this blog is to help you be reflective learners. I would like your comments about your test result and what actions you are going to take to help your progress in the subject.

The class average mark was 15/28 (53%)

Think about the following questions:

1) How much background reading have you done to support your lesson notes?
2) How much revision did you do for the test?
3) Did you find it difficult to recall facts, demonstrate understanding or apply your understanding to a new situation?
4) Have you underestimated the challenge and expectations of A Level?

Sharing your comments and ideas on this blog will help each other! I look forward to your comments.

Welcome to your blog

Hello everybody.

I thought it might be useful and fun to have a class blog.

Here we can keep a diary of what we have learnt and I hope to use it for your learning in the future.

If you have any ideas, hints, help, links then post them here, share them with the class. If you want to have a moan, complain, share your worries about the course then post them here (but try to be constructive)

I'll introduce the blog in a lesson soon.