The Structure of ATP | Biology for Grade 12 PDF Download

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Introduction

• All organisms require a constant supply of energy to maintain their cells and stay alive
• This energy is required:
  • In anabolic reactions – building larger molecules from smaller molecules
  • To move substances across the cell membrane (active transport) or to move substances within the cell
  • In animals, energy is required:
  • For muscle contraction – to coordinate movement at the whole-organism level
  • In the conduction of nerve impulses, as well as many other cellular processes
• In all known forms of life, ATP from respiration is used to transfer energy in all energy-requiring processes in cells
• This is why ATP is known as the universal energy currency
• Adenosine Triphosphate (ATP) is a nucleotide
  • The monomers of DNA and RNA are also nucleotide

ATP

• Adenosine triphosphate (ATP) is the energy-carrying molecule that provides the energy to drive many processes inside living cells
• ATP is another type of nucleic acid and hence it is structurally very similar to the nucleotides that make up DNA and RNA
• It is a phosphorylated nucleotide
• Adenosine (a nucleoside) can be combined with one, two or three phosphate groups
  • One phosphate group = adenosine monophosphate (AMP)
  • Two phosphate groups = adenosine diphosphate (ADP)
  • Three phosphate groups = adenosine triphosphate (ATP)
    

The structure of AMP, ADP and ATP

Hydrolysis & Synthesis of ATP

Hydrolysis of ATP

• Energy released during the reactions of respiration is transferred to the molecule adenosine triphosphate (ATP)
• ATP is a small and soluble molecule that provides a short-term store of chemical energy that cells can use to do work
• It is vital in linking energy-requiring and energy-yielding reactions
• ATP is described as a universal energy currency
  • Universal: It is used in all organisms
  • Currency: Like money, it can be used for different purposes (reactions) and is reused countless times
• The use of ATP as an ‘energy-currency’ is beneficial for many reasons:
  • The hydrolysis of ATP can be carried out quickly and easily wherever energy is required within the cell by the action of just one enzyme, ATPase
  • A useful (not too small, not too large) quantity of energy is released from the hydrolysis of one ATP molecule - this is beneficial as it reduces waste but also gives the cell control over what processes occur
  • ATP is relatively stable at cellular pH levels

Hydrolysis of ATP

• Hydrolysis of ATP to adenosine diphosphate (ADP) and an inorganic phosphate group (Pi) is catalysed by the enzyme ATP hydrolase sometimes called 'ATPase'
• The hydrolysis of ATP can be coupled to energy-requiring reactions within cells such as:
  • The active transport of ions up a concentration gradient
  • Enzyme controlled reactions that require energy
  • Muscle contraction and muscle fibre movement
• As ADP forms free energy is released that can be used for processes within a cell eg. DNA synthesis
  • Removal of one phosphate group from ATP releases 30.8 kJ mol -1 of energy, forming ADP
  • Removal of a second phosphate group from ADP also releases 30.8 kJ mol-1 of energy, forming AMP
  • Removal of the third and final phosphate group from AMP releases 14.2 kJ mol-1 of energy, forming adenosine
• The inorganic phosphate released during the hydrolysis of ATP can be used to phosphorylate other compounds, often making them more reactive

Features of ATP Table

ATP Synthesis

• On average humans use more than 50 kg of ATP in a day but only have a maximum of ~ 200g of ATP in their body at any given time
• Organisms cannot build up large stores of ATP and it rarely passes through the cell surface membrane
• This means the cells must make ATP as and when they need it
• ATP is formed when ADP is combined with an inorganic phosphate (Pi) group by the enzyme ATP synthase
  • This is an energy-requiring reaction
  • Water is released as a waste product (therefore ATP synthesis is a condensation reaction)

Types of ATP synthesis

• ATP is made during the reactions of respiration and photosynthesis
  • All of an animal's ATP comes from respiration
• ATP can be made in two different ways:
  • Substrate-linked phosphorylation (occurs in the glycolysis stage of respiration)
  • Chemiosmosis (occurs in the electron transport chain stage of respiration)

The Properties of Water

Water in Cells

• Water is of great biological importance. It is the medium in which all metabolic reactions take place in cells. Between 70% to 95% of the mass of a cell is water
• As 71% of the Earth’s surface is covered in water it is a major habitat for organisms
• Water is composed of atoms of hydrogen and oxygen. One atom of oxygen combines with two atoms of hydrogen by sharing electrons (covalent bonding)
• Although water as a whole is electrically neutral the sharing of the electrons is uneven between the oxygen and hydrogen atoms
  • The oxygen atom attracts the electrons more strongly than the hydrogen atoms, resulting in a weak negatively charged region on the oxygen atom (δ-) and a weak positively charged region on the hydrogen atoms(δ+), this also results in the asymmetrical shape
• This separation of charge due to the electrons in the covalent bonds being unevenly shared is called a dipole. When a molecule has one end that is negatively charged and one end that is positively charged it is also a polar molecule
• Water is a polar molecule

The covalent bonds of water make it a polar molecule

• Hydrogen bonds form between water molecules
  • As a result of the polarity of water hydrogen bonds form between the positive and negatively charged regions of adjacent water molecules
• Hydrogen bonds are weak, when there are few, so they are constantly breaking and reforming. However when there are large numbers present they form a strong structure
• Hydrogen bonds contribute to the many properties water molecules have that make them so important to living organisms:
  • An excellent solvent – many substances can dissolve in water
  • A relatively high specific heat capacity
  • A relatively high latent heat of vaporisation
  • Water is less dense when a solid
  • Water has high surface tension and cohesion
  • It acts as a reagent

The polarity of water molecules allows hydrogen bonds to form between adjacent water molecules

• Water has many essential roles in living organisms due to its properties:
  • The polarity of water molecules
  • The presence and number of hydrogen bonds between water molecules

Solvent

• As water is a polar molecule many ions (e.g. sodium chloride) and covalently bonded polar substances (e.g. glucose) will dissolve in it
  • This allows chemical reactions to occur within cells (as the dissolved solutes are more chemically reactive when they are free to move about)
  • Metabolites can be transported efficiently (except non-polar molecules which are hydrophobic)

Due to its polarity water is considered a universal solvent

High specific heat capacity

• The specific heat capacity of a substance is the amount of thermal energy required to raise the temperature of 1kg of that substance by 1°C. Water’s specific heat capacity is 4200 J/kg°C
• Specific heat capacity is a measure of the energy required to raise the temperature of 1 kg of a substance by 1^oC
• Water has a high specific heat capacity of 4200 J / Kg ^oC meaning a relatively large amount of energy is required to raise its temperature
• The high specific heat capacity is due to the many hydrogen bonds present in water. It takes a lot of thermal energy to break these bonds and a lot of energy to build them, thus the temperature of water does not fluctuate greatly
• The advantage for living organisms is that it:
  • Provides suitable habitats
  • Is able to maintain a constant temperature as water is able to absorb a lot of heat without big temperature fluctuations
  • This is vital in maintaining temperatures that are optimal for enzyme activity
• Water in blood plasma is also vital in transferring heat around the body, helping to maintain a fairly constant temperature
  • As blood passes through more active (‘warmer’) regions of the body, heat energy is absorbed but the temperature remains fairly constant
  • Water in tissue fluid also plays an important regulatory role in maintaining a constant body temperature

Latent heat of vaporisation

• In order to change state (from liquid to gas) a large amount of thermal energy must be absorbed by water to break the hydrogen bonds and evaporate
• This is an advantage for living organisms as only a little water is required to evaporate for the organism to lose a great amount of heat
• This provides a cooling effect for living organisms, for example the transpiration from leaves or evaporation of water in sweat on the skin

Properties of Water & its Role in Living Organisms Table

Cohesion and adhesion

• Hydrogen bonds between water molecules allows for strong cohesion between water molecules
  • This allows columns of water to move through the xylem of plants and through blood vessels in animals
  • This also enables surface tension where a body of water meets the air, these hydrogen bonds occur between the top layer of water molecules to create a sort of film on the body of water (this is what allows insects such as pond skaters to float)
• Water is also able to hydrogen bond to other molecules, such as cellulose, which is known as adhesion
  • This also enables water to move up the xylem due to transpiration

Inorganic Ions

• An ion is an atom (or sometimes a group of atoms) that has an electrical charge
  • An ion that has a +ve charge is known as a cation
  • An ion that has a -ve charge is known as an anion
• An inorganic ion is an ion that does not contain carbon
• Inorganic ions play an important role in many essential cellular processes
• Inorganic ions occur in solution in the cytoplasm and body fluids of organisms
  • Some occur in high concentrations and others in very low concentrations
  • The concentration of certain ions can fluctuate and can be used in cell signalling and neuronal transmission
  • Each type of inorganic ion has a specific role, depending on its properties

Properties & Roles of Inorganic Ions

• You should know the following inorganic ions, as well as their properties and roles in the body:
  • Hydrogen ions (H⁺)
  • Iron ions (Fe²⁺/Fe³⁺)
  • Sodium ions (Na⁺)
  • Phosphate ions (PO₄^3-)
  • Calcium ions (Ca²⁺)

Hydrogen ions

• Hydrogen ions are protons
• The concentration of H⁺ in a solution determines the pH
• There is an inverse relationship between the pH value and the hydrogen ion concentration
  • The more H⁺ ions present, the lower the pH (the more acidic the solution)
  • The fewer H⁺ ions present, the higher the pH (the more alkaline the solution)
• The concentration of H⁺ is therefore very important for enzyme-controlled reactions, which are all affected by pH
  • The fluids in the body normally have a pH value of approximately 7.4
  • The maintenance of this normal pH is essential for many of the metabolic processes that take place within cells
  • Changes in pH can affect enzyme structure
  • For example, abnormal levels of hydrogen ions can interact with the side-chains of amino acids and change the secondary and tertiary structures of the proteins that make up enzymes
  • This can cause denaturation of enzymes

Iron ions

• There are actually two versions of iron ions (known as oxidation states)
  • Iron (II) ions, also known as ferrous ions (Fe²⁺)
  • Iron (III) ions, also known as ferric ions (Fe³⁺)
• Iron ions are essential as they can bind oxygen
  • Haemoglobin is the large protein in red blood cells that is responsible for transporting oxygen around the body
  • Haemoglobin is made up of four polypeptide chains that each contain one Fe²⁺
  • This Fe²⁺ is a key component in haemoglobin as it binds to oxygen
  • Myoglobin in muscles functions in a similar way (it is an oxygen-binding protein) but is only made up of one polypeptide chain (containing one Fe²⁺)
• Iron ions are also essential as they are involved in the transfer of electrons during respiration and photosynthesis, so they are key to the biological generation of energy
  • Iron ions are an essential component of cytochromes (that are themselves a component of electron transport chains)
  • Cytochrome c contains an iron ion that is essential to its function
  • During the electron transport process, this iron ion switches between the Fe³⁺ and Fe²⁺ oxidation states, which allows for electrons to be accepted and donated

Sodium Ions

• Na⁺ is required for the transport of glucose and amino acids across cell-surface membranes (e.g. in the small intestine)
  • Glucose and amino acid molecules can only enter cells (through carrier proteins) alongside Na⁺
  • This process is known as co-transport
  • First, Na+ is actively transported out of the epithelial cells that line the villi
  • The Na+ concentration inside the epithelial cells is now lower than the Na⁺ concentration in the lumen of the small intestine
  • Na⁺ now re-enters the cells (moving down the concentration gradient) through co-transport proteins on the surface membrane of the epithelial cells, allowing glucose and amino acids to enter at the same time
• Na⁺ is also required for the transmission of nerve impulses

• PO₄^3- attaches to other molecules to form phosphate groups, which are an essential component of DNA, RNA and ATP
• In DNA and RNA, the phosphate groups allow individual nucleotides to join up (to form polynucleotides)
• In ATP, the bonds between phosphate groups store energy
  • These phosphate groups can be easily attached or detached
  • When the bonds between phosphate groups are broken, they release a large amount of energy, which can be used for cellular processes
• Phosphates are also found in phospholipids, which are key components of the phospholipid bilayer of cell membranes

Calcium Ions

• Ca²⁺ is essential in the movement of organisms:
  • In synapses, calcium ions regulate the transmission of impulses from neurone to neurone
• Ca²⁺ also stimulates muscle contraction
  • When an impulse reaches a muscle fibre, Ca²⁺ is released from the sarcoplasmic reticulum
  • This Ca²⁺ binds to troponin C, removing the tropomyosin from myosin-binding sites on actin
  • This allows actin-myosin cross-bridges to form when the muscle fibre contracts
• Ca²⁺ can also help to regulate protein channels, which affects the permeability of cell membranes
• Many enzymes are activated by Ca²⁺, making these ions key regulators in many biological reactions
• The presence of Ca²⁺ is also necessary for the formation of blood clots (it is known as a clotting factor)