Posts Tagged ‘Biochemistry’

Beta Oxidation

Hey guys,
So the project for Biochemistry this semester was a video project. My group decided to based our video on Beta oxidation, giving the necessary steps and explaining them in detail. Please give us your support by looking at the video and commenting if you so desire.

Many Thanks.

Brandon.

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This quiz is purely on enzymes only.

1. What class of enzymes breaks down substrates by adding or losing, hydrogen and oxygen?

A) Hydrolases

B) Transferases

C) Oxidoreductases

D)Ligases

 

2. Ligases is the only one of the six major classes of enzymes to

A) Undergo hydrolysis

B) Combine molecules

C) Oxidise a substrate

D)Rearrange the structure of a substrate.

 

3.Uncompetitive Inhibitors binds to

A) Active site only

B) Enzyme-substrate complex only

C) Both the free enzyme and enzyme-substrate complex

D) To the substrate molecule only

 

4. Mixed Inhibitors binds to either the free enzyme or to the enzyme-substrate complex. How does this affect Vmax and Km?

A) Nothing is affected

B) Vmax increases and Km can increase and decrease

C) Vmax is reduced and Km can increase and decrease

D) Vmax remains constant, while Km increases

 

5) Which type inhibitor binds only to the active site?

A) Non-competitive

B) Uncompetitive

C) Competitive

D)Mixed

 

Best of luck.

Thank you for you time.

What is an Inhibitor?

An inhibitor is any substance that diminishes the velocity of an enzyme catalysed reaction.

There are two main categories of inhibition- Reversible and Non-reversible. This entry deals with reversible inhibitors only. There are four types of reversible enzymes.

These are:

  • Competitive Inhibtors
  • Non-competitive Inhibitors
  • Uncompetitive Inhibitors
  • Mixed Inhibitors

 

Competitive inhibitors.

These inhibitors compete with the substrate molecules for the active site of the enzyme. Competitive inhibitors only bind to the active site of the free enzyme, note that it never binds to the enzyme-substrate complex. Competitive inhibitors do not change the Vmax, maximum velocity, of the reaction, however the substrate affinity binding to the active site of the enzyme, decreases. This means Km increases. (Remember high affinity = low Km and vice versa) .

In the case of allosteric enzymes. Both substrate and inhibitor cannot bind to the enzyme at the same time. When the Inhibitor binds to one active site, it temporarily changes the shape of the other active site, preventing the substrate from binding.

Taken from "Describe an Induced fit model" , www.tokresource.org

Taken from “Describe an Induced fit model” , http://www.tokresource.org

 

Non-Competitive Inhibitors.

Unlike competitive inhibitors,which only bind to the active site of the enzyme, non-competitive inhibitors can bind to the free enzyme as well as the enzyme substrate complex. Since the substrate can still bind to the enzyme, this tells us that Km is unchanged, however Vmax is reduced as the enzyme does not function with the inhibitor.

 

Uncompetitive Inhibitors.

These inhibitors only bind to the enzyme substrate complex. This means that the substrate can bind to enzyme although the inhibitor is already bound to it. This also tells us that both Vmax and Km are reduced.

 

Mixed Inhibitors.

Mixed inhibitors get the term “mixed” because they can act as competitive inhibitors, and only bind to the active site, or act and uncompetitive inhibitors and bind to the enzyme substrate complex. As a result of this, substrate affinity to the enzyme can either increase or decrease,(i.e. low or high Km values). From uncompetitive inhibitors, Vmax will always be reduced as the presence of the inhibitor decreases the velocity.

Factors affecting the velocity of the reaction are:

  • Substrate concentration [S]
  • Enzyme concentration [E]
  • Temperature
  • pH

Velocity is measures by : Amount of substrate ÷ time taken

How does temperature affect velocity?

All enzymes work at a optimum temperature, meaning that a slight raise above or decline, will cause the enzyme to stop working.

add_ocr_bi02005a

Denaturation- Denaturation is a co-operative process, if one bond breaks it causes a chain reaction, leading to all bonds breaking. In this event, the bonds broken are hydrophobic bonds, disulphide bonds and ionic bonds. ( Please refer to older post on amino acids and proteins to see how these bonds are formed).

pH

pH affects the ionization of the enzyme. Functional groups such as the amine group can be dissociated into a anion or cation. Ionic baonds are mostly affected by pH.

i72_enzyme_ph_graph

The descending slope after the optimum pH shows enzymes being denatured. So we can also so as pH increase or decrease, of the optimum temperate, enzymes activity decreases.

Michaelis-Menton Curve

enzmichaelis

This curve shows how velocity varies with substrate concentration.

Assumptions to M-M curve.

  1. Relative concentration of enzymes and substrates ( [E] and [S]), all active sites are saturated
  2. Steady state assumption: The rate of formation is equal to the rate of substrate breakdown.
  3. Initial velocity, Vo, will measure rate at the start of the reaction. (i.e To = Vo)

Km, is a michaelis-menton constant. It is equivalent to [S]= Vmax ÷ 2. It reflects the affinity of the enzyme for that substrate. ( Higher the Km, lower the substrate affinity and vice versa.

Vmax, is the maximum velocity or rate at which happens when all actives sites are saturated.

 

Lineweaver- Burke plot.

Lineweaver_Burk

A Lineweaver- Burke Plot is a double reciprocal plot. It is always in straight lines. The point of the line where y intercepts is know as Vmax. Notice how all labels are the reciprocal of their’ nomal state.

They do, in fact there are four levels of protein structures: primary, secondary, tertiary and quaternary.

Primary structure of proteins.

Image

Fredrick Sanger was the first scientist to discover the primary structure of proteins, by looking at the protein, insulin. The specific sequence of amino acids in a polypeptide chain is known as the primary structure of proteins. Peptide bonds are the only bonds involved in this sequence.

Secondary structure of proteins.

Image

Secondary proteins, are the shape taken up by the polypeptide chain due to hydrogen bonding. The two most common shapes of secondary proteins are the α-helix and the β-pleated sheets.

An α-helix chanin twist every 3.6 amino acid. It is formed due to the formation of hydrogen bonds  between the CO of one amino acid to the NH of the fourth amino acid.

β-pleated sheet are formed among adjacent polypeptides chains. Like α-helices, hydrogen bonds form between the CO and NH of neighbouring chains, which results in a stronger, yet less elastic structure.

 

Tertiary structure of Proteins.

Three types of bonds, formed between R-groups, are responsible for the shape of these proteins. These bonds are hydrogen bonds, ionic bonds, and disulphide bonds.

Hydrogen bonds, most common, is formed when an electronegative oxygen is attracted to the electropositive hydrogen of another R-group.

hydrogenBond

Ionic bonds are formed between an charged amino acid and carbonyl group.

Capture

Disulphide bond is a covalent bond formed through oxidation of two -SH groups.

Ch2A3

These bonds cause proteins to fold into compact, globular shapes. These proteins are soluble and are called globular proteins, for example, insulin is a globular protein.

Note: Proteins such as keratin or collagen are insoluble and do not fold into tertiary structures, instead they remain unfolded into non-fibrous structures. These are called fibrous proteins.

 

Quaternary structure of proteins.

Quaternary structure of proteins is the combination of two or more proteins. An example of this type of structure is haemoglobin, which is a combination for four proteins.

hemoglobin

Proteins are huge molecules made up of many polypeptide chains. They are seven classes of proteins. Proteins for storage, channel proteins, structural proteins, proteins for immune responses, enzymes, transport proteins, and receptor proteins. Proteins can be globular, fibrous, or membranous.

Receptor proteins are used to sense stimuli.

Image

Channel proteins aid in controlling molecules in and out of the cell. Channel proteins allows simple diffusion into the cell.

Transport proteins carry valuable resources around the body eg. Haemoglobin transport oxygen.

 

Structural proteins, cartilage made up of the protein collagen, helps prevent bones from rubbing together and cause damage.

Proteins in charge of immune responses, such as antibodies, fight off infection and foreign contaminants from harming the body.

Enzymes are used to speed up biochemical reactions in the body, that may take too long than life itself.

 

 

A peptide bond (C-N) is formed when the α-amino group of one amino acid and the carboxyl group of the other amino acid combines, covalently, via condensation.

Image

Peptides.

Peptides get their name from the peptide bonds between two or more amino acids. They are grouped accordingly to the number of amino acids found in the chain.