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ATP and Energy
ATP

ATP and Energy

ATP is a phosphorylated molecule made up of 3 parts:

  • Adenine: A nitrogen containing Organic base
  • Ribose: A sugar molecule with a 5-carbon ring structure (pentose sugar) acting as a backbone
  • Phosphate A chain of three phosphate group

ATP is a nucleotide, it has strong bonds between the phosphates, therefore providing large amounts of energy when these bonds are broke. (albeit small in comparison to glucose)

Formation of a ATP synthase (or phosphorylation) 

ATP                 +             H2O                        ->                      ADP                 +             P          (+ energy)

Adenosine                         Water                                           Adenosine                    Phosphorus

Triphosphate                                                                           diphosphate

Water is required to breakdown the ATP molecules requiring the Enzyme ATPase (or ATP Hydrolase), thus being a hydrolysis reaction.

In phosphorylation, the adding of phosphate to ADP to create ATP

  • There are 3 forms:
  • Oxidative phosphorylation

Occurs in the membrane of mitochondria during aerobic respiration and provides the process of the electron transport chain

  • Phosphorylation

Occurs in the thylakoid membrane in the chloroplast of plants only

  • Substrate-level phosphorylation

Occurs when phosphate groups are transferred from donor molecules to ADP to make ATP (e.g. in glycolysis)

ATP vs Glucose

  • ATP is more immediate than glucose as hydrolysis reactions are quick
  • ATP to ADP is a single reaction, thus quicker however less energy is produced. ATP is more suitable for tasks that require a quick response in energy, however not in massive yields.
  • Glucose is a complex reaction, therefore slower, however produces far more energy

Which reactions require ATP?

  • Metabolic process
  • Movement (muscle contractions)
  • Active transport
  • Secretion
  • Activation of molecules
  • Bioluminescence

ATP is a phosphorylated molecule made up of 3 parts:

  • Adenine: A nitrogen containing Organic base
  • Ribose: A sugar molecule with a 5-carbon ring structure (pentose sugar) acting as a backbone
  • Phosphate A chain of three phosphate groups

 

ATP is a nucleotide, it has strong bonds between the phosphates, therefore providing large amounts of energy when these bonds are broke.

 

ATP properties:

  • ATP stores a small unit of energy which is both suitable for the reactions which requires it as well as minimal energy is wasted as heat
  • ATP is a small soluble molecule and therefore can easily be transported around the cell
  • The ATP molecule is easily hydrolysed and so energy release is fast
  • ATP is a simple molecule to reform
  • ATP allows for other molecules to become more reactive as it can transfer one of its phosphate groups to them in phosphorylation
  • ATP does not leave the cell it is produced in

 

 

 

 

 

 

Triglycerides
Triglycerides

Triglycerides

 

Triglycerides

  • Triglycerides are made up of 3 fatty acid chains attached to a glycerol molecule
  • They are bonded by an ester bond formed through condensation reactions
Triglycerides diagram

Triglycerides diagram

Triglycerides are formed under condensation reactions between Glycerol (C3H8O3) and fatty acids. The result of this reaction is a water molecule that forms one part of the triglyceride, with 3 forming together though an ester bond.

Saturated: C-C

Unsaturated: C=C

Saturated Fatty Acids

  • Every Carbon atom is bonded to as many hydrogen atoms as possible, no more can be added hence they are “saturated with hydrogens”
  • Triglycerides consisting of saturated fatty acids can pack together to form solid fats at room temperature
  • Carbon chains are straight with no kinks
  • Mainly food in animals and dairy products contain saturated fats

Unsaturated Fats

  • Triglycerides consistent of a “kink” in its chain at the double bond point.
  • They do not pack together easily, and form liquid oils at room temperature
  • The more double bonds, the more kinks it will have in the chain
  • Double bonds introduce a definite “kink” in the carbon atom chain
  • Not every carbon atom are bonded to as many hydrogen atoms as it could be – hence unsaturated (with hydrogen) there are double bonds
  • Mainly found in vegetable oils, nuts and fish

Triglycerides are lipids that are an important source of energy for the body. Triglycerides are broken down and reassembled in the body.

Enzymes
Enzyme

Enzymes

Enzymes

Enzymes are made up of proteins, they are biological catalysts.

They increase the rate of metabolic reactions. Nearly all of the reactions in the body use an enzyme, when a reaction involving an Enzyme occurs, a Substrate is turned into a Product. The Substrate can be one or more molecules. The Active Site of an Enzyme is Complementary to the Substrate it catalyses.

They are soluble in water to hydrophilic side group

They very large molecules, but only small parts of the molecules act as the catalyst

Enzymes are specific are specific to one type of reaction Enzymes. All enzymes are Globular Proteins with a specific Tertiary Shape. The rest of the Enzyme is much larger and is involved in maintaining the specific shape of the Enzyme.

Enzymes in respiration

Hydrogen peroxide is a product of respiration, enzymes are required to break down this as it is harmful

Hydrogen Peroxide         ->             Water                                +             Oxygen

                         4H2O2                                                                      4H2O                                     2O2

The use of catalase is used to break down Hydrogen peroxide down into water and oxygen

a) Measure 25 cm3 of hydrogen peroxide solution into each of three conical flasks.

b) At the same time, add a small piece of liver to the first flask, a small piece of potato to the second flask, and a small piece of celery to the third flask.

c) Hold a glowing splint in the neck of each flask.

d) Note the time taken before each glowing splint is re-lit by the evolved oxygen.

e) Dispose of all mixtures into the bucket or bin provided.

 

Extracellularly and intracellularly

Extracellularly are enzymes that is secreted by a cell and functions outside of that cell. Many enzymes secreted in digestion are extracellularly such as amylase or pepsin.

Intracellularly are enzymes that functions within the cell in which it was produced

DNA replication is intracellularly

All reactions require energy before they can start.  It is shown as activation energy.  This starts in breaking bonds of the reactants: enzymes lower this activation energy. This creates a transition state between enzymes and substances that are more stable.

Lock and Key Theory

Active sites are a small area with a specific shape to the substrate of the substance. The shape of the Active Sites of Enzymes are exactly complementary to the shape of the Substrate.

Enzymes that bonds with the correct substrate form enzyme substrate complex. The enzyme will catalyse the reaction, and the products, together with the enzyme, will form an Enzyme-Product Complex. According to this model, it is possible for an enzyme to catalyse a reverse reaction.

 

Structure

Structure

 

Induced Fit Theory

The active site is not the exact size of the substrate, but change shape in the presence of a specific substrate to become Complementary.

As the substrate moves closer to the enzyme it is ‘moulded’ around the substrate. This tight envelope of the substrate forms enzyme substrate complexes. When a substrate molecule collides with an enzyme, if its composition is specifically correct, the shape of the enzyme’s Active Site will change so that the substrate fits into it and an Enzyme-Substrate Complex can form. The reaction is then catalysed and an Enzyme-Product Complex forms.

Structure

Structure

Enzyme actions

For enzymes to work they require:

  • Physical contact with substrate
  • Must have correct shaped active sites

Measuring Enzyme action

  • Rate of the formation of products

 

Structure

Formation

 

  • Rate of Disappearance

Structure

 As the enzyme reacts with the substrate of the molecule, the mass of the substrate decreases as the amount of product increases over time

Graph 1 shows that at the beginning there is lots of substrate, when these substrates bond to the active sites the reaction begins. This process occurs rapidly causing amount of product to rise quickly and the amount of reactant to fall too, as shown in graph 2. The curve levels of nearer the end as a result of the amount of substrates was reducing. The decreased concentration of substrates causes the drop off of amount of product produced, this is the result of the enzyme finding it harder to find a substrate molecule that haven’t been reacted yet as well as products of previous reactions being in the way.

Rate of enzyme actions

  • Temperature

Lower temperatures means there is less kinetic energy in the molecules, so fewer successful collisions occur.

Optimum temperature for enzymes is the maximum amount of kinetic energy, thus successful collisions, before the enzyme begins to denature to excessive heat.

At high temperature there is an increase in kinetic energy and heat which causes the breakdown of hydrogen bonds, denaturing the tertiary structure of the active site and enzyme shape. At first enzymes fit less easily, therefore there is a slower rate of reaction.

Structure

pH

Only extreme pH causes denaturing

pH affects the amino acids of the enzyme as it changes the charge of them. This causes different molecules to bond to it, as a result the active site is different. This alters the tertiary structure.

Fluctuations in internal pH of small amounts does little however

Structure

Concentration of Enzymes

Low enzyme concentration means there are fewer active sites occupied. This means more active sites are available.

Increased enzymes concentration means more active sites available and the reaction can produced at a faster rate due to more successful collisions

Eventually increasing the enzyme concentration beyond a point means that there are too many enzymes to substrate.

 

Structure

Structure

 

  • Substrate Concentration

Low substrate concentration means there are fewer substrate sites occupied. This means more substrates are available.

Increased substrate concentration means more substrates available and the reaction can produced at a faster rate due to more successful collisions

Eventually increasing the substrate concentration beyond a point means that there are too many substrate to enzymes

Structure

Amino Acids
Amino Acids

Amino Acids

Amino Acids
Amino acid is a monomer.
chain of amino acids form polypeptides/dipeptides

Different amino acid have different R groups attached to them. The amino acid carboxyl group stays the same.
here are 20 amino acids naturally incorporated proteins:
Valine, Leucine, Alanine, Arginine, Proline, Cysteine, Threonine, Methionine, Histidine,
Glutamine, Lysine, Aspartic acid, Glutamic Acid, Serine, Phenylalanine, Tyrosine, Tryptophan, Asparagine, Glycine,
There are 8 amino acids which must be consumed through foods:
Histidine, Lysine, BCAAS (Branched Chain amino acid), Phenylalanine, Methionine
Dipeptides are formed by 2 amino acids in a condensation reactions.

Biological Molecules
Biological Molecules

Biological Molecules

Biological Molecules

Monomer

A monomer is a single unit of covalent bonds, which when strung together make a polymer. They are low in molecular weight which can combine together.

Proteins are made up of repeating amide, these are called polyamides. Likewise, nucleotides are the monomer units of DNA and RNA and the cellulose is made up of repeating β-glucose units.

Polymer

 A polymer is a chain of monomers, these giant molecules are known as macromolecules. Polymers are usually made up of about 50 monomers. Macromolecules vary as a result of different arrangements of these monomers.

The 4 simple groups of carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates – composed of sugar monomers and necessary for energy storage.

Lipids – include fats, phospholipids and steroids. Lipids help to store energy, cushion and protect organs, insulate the body and form cell membranes.

Proteins – composed of amino acid monomers and have a wide variety of functions including molecular transport and muscle movement.

Nucleic Acids – include DNA and RNA. Nucleic acids contain instructions for protein synthesis and allow organisms to transfer genetic information from one generation to the next.

Carbohydrates – composed of sugar monomers and necessary for energy storage.

Lipids – include fats, phospholipids and steroids. Lipids help to store energy, cushion and protect organs, insulate the body and form cell membranes.

Proteins – composed of amino acid monomers and have a wide variety of functions including molecular transport and muscle movement.

Nucleic Acids – include DNA and RNA. Nucleic acids contain instructions for protein synthesis and allow organisms to transfer genetic information from one generation to the next.

Condensation Reaction

Condensation reactions is when two molecules join together to form a larger molecule, and a small bi-product, for example in a dehydration reaction this product is usually water. Other bi products include hydrogen chloride, methanol or acetic acids. Condensation reactions are used in the production of polymers.

When the two molecules react, the condensation is called intermolecular. An example of this is the condensation of 2 amino acids to form the peptide bond; characteristics of proteins.

If the reaction is between atoms or groups of the same molecules, the condensation is called intramolecular. A famous example of this is the Dieckmann condensation where two ester groups of a single diester molecule react to each other to lose a small alcohol molecule and form a β-ketoester.

Hydrolysis Reaction

Hydrolysis reactions is the breaking down of large molecules into smaller ones by the addition of a water molecule, for example converting polysaccharides to monosaccharaides with the addition of water.

Introduction to Biology

by Sean 0 Comments

Biology
an introduction
Biology is a massive subject area with many branches, most of which I don’t particularly understand…
Nonetheless, let us begin
We have 6 key areas for you to rummage through, starting from our first unit on Biological molecules right through to
I strongly reccomend you take a look at our specification here: Specification
 

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