P3- Biochemical ProcessesProcesses within cells

Key KnowledgeThe nature of biochemical processes within cells Catabolic and anabolic reactions – reactions

releasing or requiring energy Role of enzymes as protein catalysts The role of ATP and ADP in energy

transformations Requirements for photosynthesis Requirements for aerobic and anaerobic

cellular respiration

Chemical reactions in cellsIn the cell reactions happen in steps- A biochemical pathway.

This allows for management of energy requirements.

Each step is controlled and facilitated by protein catalysts and coenzymes.

Cellular Metabolism This refers to the thousands of chemical

reactions that occur constantly in each living cell.

Heat is generated by the activity of cells as they break down and build molecules.

All metabolic reactions that occur in cells are controlled and regulated to maintain cell functions and to meet the energy needs of a cell.

A biochemical pathway. Each step is controlled by an enzyme.

Key metabolic pathways include: Photosynthesis Cellular Respiration

http://highered.mcgraw-hill.com/olc/dl/120070/bio09.swf

It is important the products don’t build up in a cell as it can inhibit the cells function:

In plants glucose from photosynthesis is converted to starch which is stored by the plant.

In animals the products of cellular respiration diffuse from cells and release into the atmosphere.

Types of reactions: Anabolic: a reaction that builds up complex

molecules from more simple ones.

Catabolic: reactions, such as cellular respiration, that involve the breakdown of complex molecules to simpler products.

Aerobic: a reaction that requires oxygen. Anaerobic: a reaction that doesn’t require

oxygen. Endergonic: an energy requiring chemical

reaction. Exergonic: a reaction that releases energy.

In endergonic reactions (reactions that absorb energy) – total net amount of energy is absorbed and locked up in the bonds of the products, which have more stored energy than the reactants.

In exergonic reactions (reactions that release energy) – total net amount of energy is released from the bonds of the reactants and the products have less energy than the reactants.

Types of reactions:

The amount of energy needed for the reaction to occur is known as activation energy.

Anabolic Catabolic Endergonic

Exergonic

PhotosynthesisCellular respiration

The energy shuttle Cells capture the chemical energy released

from exergonic reactions to fuel endergonic reactions.

These two reactions occur simultaneously in cells.

In this process some energy is lost as heat, which escapes from the cells into the atmosphere.

Reactions don’t always occur in the same place within the cell, energy needs to be transferred between reactions.

ATP: Adenosine triphosphate ATP is the universal primary source of free energy for all

living organisms. ATP contains adenosine attached to a sugar group (ribose),

which is bound to a chain of three phosphate groups.

ATP is a well designed renewable energy source. When a cell requires energy to drive an endergonic reaction, the high energy chemical bonds attaching to the last phosphate group is broken, thus releasing stored energy

ATP ADP The energy that was held in that bond (now broken) is

able to fuel a cellular reaction. The remaining molecule now has only two phosphate

groups and is called ADP (adenosine diphosphate). This reaction is sped up by the enzyme ATPase.

... and in reverse Free energy obtained from

an exergonic reaction can also be used to add a phosphate group to ADP, converting it to ATP. The ATP-ADP cycle is the cells way of shuttling energy between reactions.

The addition of a phosphate group to an organic molecule of any sort is called phosphorylation.

DefinitionsATP: a molecule

that released energy for cellular reactions when its terminal phosphate group is removed.

ADP: a compound composed of adenine and ribose with two phosphate groups attached; it is converted to ATP for energy storage when it gains a phosphate group (phosphorylation).

Characteristics of enzymes Only a small amount of enzyme is needed to

do a big job. They are not used up in the reaction. Can be re-used over and over.

An enzyme doesn’t change the direction of the reaction, but does speed up the reaction.

Make the reaction occur more easily by reducing activation energy.

An enzyme won’t change the final amount of product formed.

Are proteinsAre substrate specific

Enzymes Are ProteinsThe enzyme binds to the substrates by its active site

The active site is a pocket formed by the folding of the proteinwhere the substrates bind.

How enzymes bind their substrates The active site of an enzyme has a shape that

complements the shape of the binding site of the substrate; that is, they ‘fit together’ like pieces of a jigsaw puzzle.

Two models exist to describe the mechanism of an enzyme binding with it’s substrate.

These are: Lock and key model Induced fit model has been refer red

http://scholar.hw.ac.uk/site/biology/activity6.asp

Induced fit hypothesis

Enzyme specificity is at the heart of how enzymes control each step in a biological pathway.

What allows proteins to be so specific in their function?

Enzymes Even though enzymes are manufactured inside

cells, their site of function may be either within the cell (intracellular) or outside the cell (extracellular).

Intracellular enzymes speed up and control metabolic reactions inside the cell.

Extracellular enzymes are secreted from the cell and catalyse reactions outside the cell. For example, digestive enzymes are secreted from specialised cells in the lining of the gut but act on food in the gut.

Naming enzymes It is usually easy to tell if a substance is an

enzyme, they often have the suffix – ase eg: protease, lipase, amylase, nuclease, ATPase etc.

Unfortunately, there is always an exception to the rule

eg: pepsin and trypsin, found in the mammalian gut and work on breaking down protein.

Substrate Enzyme ProductHydrogen peroxide

Catalase Oxygen and water

Starch Amylase MaltoseMaltose Maltase GlucoseProtein Pepsin PeptidesPeptides Protease Amino acidsFats Lipase Fatty Acids and

Glycerol

Enzymes lower activation energy

Enzyme power Adding ferric ions (Fe3+) to

hydrogen peroxide increases rate of decomposition and therefore make it less toxic.

Catalase – a catalytic protein, one of the fastest, found in the liver. It contains a Fe ions which speed up decomposition of hydrogen peroxide to water and oxygen by 100million times, making it less toxic.

This ability to lower the activation energy needed is why enzymes are so important.

Enzyme power Enzymes generally work rapidly.

Catalase: one of the fastest acting enzymes. It is found in several organs and tissues, including the liver, where its job is to speed up the decomposition of hydrogen peroxide (H2O2) into oxygen and water.

2 H2O2 2H2O + O2

Enzyme power Hydrogen peroxide is a toxic by-product of

metabolism so it is essential that the cell removes it quickly.

Hydrogen peroxide has a high activation energy, which means that the energy needed to decompose it to water and oxygen is high.

Enzymes – fast workers Enzymes are large globular

proteins. Earlier we looked at the

formation of proteins. At the tertiary structure the protein has its definitive shape. During this stage in an enzyme a pocket or groove is formed (usually made by a beta pleated sheet).

This groove or pocket can accommodate one or more specific substrate molecules and is called the active site.

The active site is highly specific for a particular substrate. This model of enzyme action is known as the lock and key model.

Enzymes – fast workers The bonds that form between

an enzyme and the substrate can also modify the shape of the enzyme so that the substrate can be fully accommodated.

This is knows as the induced fit model of enzyme action.

It is important to note that enzymes are generally proteins, but not always eg: ribozymes

http://www.youtube.com/watch?v=V4OPO6JQLOE

Coenzymes & cofactorsThe catalytic activity of many enzymes also depends upon the presence of metallic cations. Cations that bind to an enzyme, and increase the rate of catalysis are called cofactors

Coenzymes assist catalysis by binding to enzymes or by functioning as carriers of electrons and protons. They may also carry specific atoms or groups of atoms, such as phosphate, that are required for or produced by chemical reactions

Cofactors: small inorganic substances (e.g. zinc ions and magnesium ions) that need to be present in addition to an enzyme to catalyse a certain reaction

Coenzymes: non-protein organic substances that are required for enzyme activity.

Small molecules compared to the enzyme

Major role in metabolic pathways

Can function as a carrier, donor or acceptor of a substance involved in the reaction and/or may bind with an enzyme to activate it.

Important Coenzymes

COENZYMEABBREVIATION

FUNCTIONLoadedform

Unloadedform

Adenosine triphosphate ATP ADP Energy transfer

Nicotine adenine dinucleotide(based on the vitamin niacin)

NADH NAD+ Transfer of electrons and protons

Nicotine adenine dinucleotide phosphate(based on the vitamin niacin)

NADPH NADP+ Transfer of electrons and protons

Flavine adenine dinucleotide(based on the vitamin B12)

FADH2 FAD Transfer of electrons and protons

Key Knowledge Cellular Metabolism: the

thousands of cellular reactions that occur constantly in living cells.

Biological Pathway: series of steps in a reaction where the product from one step becomes the reactant for the next, each step is regulated by an enzyme.

Aerobic – in the presence of oxygen

Anaerobic – in the absence of oxygen

ATP: Endergonic = Catabolic : ADP

ADP: Exergonic = Anabolic : ATP

ATPase releases the third phosphate to turn ATP to ADP and the process of phosphorylation attaches a third phosphte to ADP to create ATP.

Activation energy: the amount of energy needed for a reaction to occur (enzymes are so effective as they are able to lower this activation energy to get the reaction started quicker).

Products need to be removed from the cell so that they do not build up and slow down vital metabolic reactions.

Key Knowledge Enzymes are organic

catalysts (speed up reaction).

Generally proteins, however not always eg: ribozymes.

Enzymes are recycled.

Intracellular enzymes: work within the cell.

Extracellular enzymes: created in a cell and then excreted to work outside of the cell.

Enzymes generally end with the suffix ‘ase’ eg: lipase, amylase.

Beta folded sheets created in secondary stage of protein production become the enzymes active site.

The active site of the enzyme binds with the substrate of the reactant. Highly specific: lock and key model.

When the active site and substrate binds the enzyme can change shape, this is knows as the induced fit model.

Enzymes need help: cofactors (inorganic substances eg: zinc)and coenzymes (non protein organic substances).

Factors that influence enzyme activity

Factors that influence enzyme activity include: pH Temperature Inhibitors Enzyme concentration Substrate concentration Cofactors and coenzymes

Factors effecting enzyme capabilities Enzymes are sensitive:

The optimum temperature for an enzyme is that in which they naturally occur in.

For most of the enzymes associated with plants and animal metabolism, there is little activity at low temperatures – it slows down the number of collisions, but doesn’t denature the enzyme.

As the temperature increases, so does the enzyme activity. This is because as the temperature increases molecules become more excited and collide more often. This increase in collisions increases the opportunity for a substrate to bump into its enzymes active site.

However, if the point is reached where the temperature is too high and the enzyme structure is damaged, the enzyme ceases to function; this is called enzyme or protein denaturation.

Factors effecting enzyme capabilities Poisons often work by denaturing

enzymes or occupying the enzyme’s active site so that it does not function.

Some enzymes will not function without cofactors, such as vitamins or trace elements.

A change in pH affects the amino acid chain of a protein.

As a solution becomes more basic, proteins tend to lose hydrogen ions. In acidic solutions, proteins gain hydrogen ions.

Buffered solution: weak acid, are better solutions for chemical reactions that water (neutral) due to the H being released from the acidic solution, creates a buffer for H or OH being released.

If the charges on the amino acids in a protein are changed, then the bonds that maintain the three-dimensional structure of a protein can be changed.

For example... Pepsin in the stomach

(pH1.5).

Catalase works in a neutral environment of cells in the liver (pH 7).

Alkaline Phosphatase in bone (pH 9.5).

Effect of having more substrate... The amount of substrate present in a reaction can

limit the amount of product produced. More substrate will result in more product until all

enzymes are working at their maximum capacity (enzyme saturation)

Effect of having more enzyme... When the amount of enzyme in a system is

increased, then the amount of product increases until:

the product starts to inhibit enzyme action the substrate is depleted.

The rate of reaction is proportional to the enzyme concentration provided there is enough substrate present.

pH affects enzyme activity The pH scale is 1–14, where 1 is very acidic, 14 is

very basic, 7 is neutral. The optimum pH for an enzyme is that at which

the enzyme shows maximal activity. Each enzyme has an optimum pH (enzymes are

very sensitive to pH). Changing pH affects enzyme function because

hydrogen bonds break, and therefore the 3D shape of the enzyme changes.

pH affects enzyme activity Different enzymes have different optimum pH values. For example, in the stomach the enzyme pepsin has a low

optimum pH, so the stomach produces acid to maintain this low pH. The enzymes of the pancreas need a higher pH to work.

Temperature affects enzyme activity Warming increases the rate of most chemical

reactions, including enzyme catalysed reactions. Extra heat energy is taken up by molecules so they

move faster. This increases the rate of interaction between substrate and enzyme.

Lower temperatures meant that molecules move more slowly. This decreases the rate of interaction between substrate and enzyme.

Although temperatures either side of the optimum temperature will decrease enzyme activity, extremes of heat and cold have different effects.

Temperature affects enzyme activity Most enzymes have an optimum temperature range, which

is the temperature at which the enzyme’s catalytic activity is greatest.

Temperatures outside the optimum temperature range will decrease enzyme activity.

Temperature affects enzyme activity The rate of enzyme activity increases with increasing

temperature until the enzyme begins to denature or break down.

The temperature at which denaturation begins is referred to as the critical temperature of an enzyme.

Denaturation means that the tertiary structure of the protein is permanently changed and cooling it back down again won’t restore the enzyme’s function.

In contrast, enzymes are not denatured when it is too cold.

Enzymes that are inactivated because of low temperatures become active again when the temperature is returned to normal.

Different types of inhibitors Competitive inhibitors

Inhibitory molecule competes with the substrate for the active site.

Slow down enzyme activity by blocking substrate binding to active site.

Non-competitive inhibitors Allow the substrate to bind to the active site. Slow down enzyme activity by binding elsewhere

to enzyme.

Inhibitors An inhibitor is any chemical that changes the shape of

the active site of the enzyme so that it has a lower affinity for substrate.

Inhibitors may be reversible or irreversible. Reversible inhibitors are used to control enzyme

activity as they only temporarily deactivate enzymes.

Heavy metals such as lead, mercury and arsenic are toxic because they are irreversible inhibitors of enzymes.

Inhibition may be competitive, non-competitive or allosteric.

Regulating enzyme affinityAffinity refers to the ease with which

the enzyme binds with a substrate.Cells do this by attaching other

molecules to the enzyme to change the shape of its active site.

This allows cells to increase or decrease the rate of reaction in particular circumstances.

Enzyme concentration The rate of enzyme

activity increases with increasing enzyme concentration.

Increased enzyme concentration will increase the rate of reaction.

Increased enzyme concentration will not increase the amount of product formed.

Substrate concentration Increased substrate

concentration will increase the amount of product formed.

Increased substrate concentration will increase the rate of reaction up to the point when the enzyme is saturated with substrate.

Enzymes and disease Several inherited diseases involve an inability to manufacture a particular

enzyme required to break down substances that are normally part of the diet.

Examples include: galactosaemia, lactose intolerance and phenylketonuria.

Galactosaemia due to an error (mutation) in the gene responsible for producing

one of the enzymes needed to convert galactose to glucose-1-phosphate.

Galactose accumulates in the blood and present in their urine. The liver becomes enlarged, cataracts form, growth is slow and mental development is retarded.

Sufferers who are left untreated do not often live beyond infancy. The treatment for galactosaemia is simple and largely successful

if it is commenced soon enough. All foods containing galactose, chiefly milk and milk pro ducts,

must be excluded from the diet.

Two very important chemical reactions The importance of enzymes, and the linkage between

endergonic and exergonic reactions is highlighted when we study photosynthesis and cellular respiration.

Photosynthesis is an endergonic reaction. Cellular respiration is an exergonic reaction.

Enzyme regulation Enzyme concentrations are

regulated in response to the need of the cells.

The regulation is achieved by: controlling the production breaking down the enzyme inactivating the enzyme

For example: pepsinogen is the dormant form or pepsin (enzyme that breaks down protein), it only becomes pepsin when it is introduced into the acidic stomach environment.

Enzyme regulationAn enzyme can have more than one active site if they are composed of more than one polypeptide chain – therefore they can catalyse more than one reaction = increased efficiency.

Inhibiting the work of enzymes Some enzymes have two or

more active binding sites.

Activity of almost every enzyme in a cell is regulated by feedback inhibition where the product of the reaction can inhibit enzyme activity.

Inhibitor binds to enzyme active site or allosteric site changing shape, therefore cannot bind to substrate.

http://highered.mcgraw-hill.com/olc/dl/120070/bio10.swf

http://www.youtube.com/watch?v=cbZsXjgPDLQ

Inhibitors Non-competitive

inhibitor: a molecule that binds to an enzyme at a site other than the active site which changes the shape of the enzyme so that the substrate can no longer bind to the active site.

Competitive inhibitor: a substance that competes with a substrate for an enzyme’s active site.

Examples: poisons whereby the inhibitor binds to the active site preventing the enzyme from catalysing reactions and overtime this concentration of enzyme reduces and the reactions stop.

Photosynthesis

Occurs in the chloroplast. Two stages Light dependent (occurs in

the thylakoid membrane – grana)

Light independent (occurs in the stroma)

Light dependent Light energy is absorbed by chlorophyll.

The energy absorbed energises the electrons in the water molecules, which breaks the water molecules apart.

Each water molecule is broken up into: 2 H+ (protons) 2e- 1 O

Light dependent• Oxygen is released

• Electrons make an electron transport chain, which creates the energy (ATP).

• Phosphorylation occurs so ADP + Pi changes to ATP, this is also shuttled off to the light dependent stage.

• Hydrogen ions and electrons are picked up by carrier molecule NADP to create NADPH and shuttles the hydrogen ions to the light independent stage that occurs in the stroma

Light dependent

Light dependent summaryInputs OutputLight energy (absorbed by chlorophyll)

Oxygen gas

Water NADPHATP

Light independent Could not occur without the light dependent as it relies on

NADPH and ATP. Occurs in the stroma. Calvin-Benson cycle – ATP from light dependent stage is used

to drive this process. CO2 is joined (carbon fixation) to a 5 carbon molecule circulating

in the cycle (ribulose biphosphate RuBP), rubisco aids this process.

A 6 carbon molecule is formed, but is unstable. 6 carbon molecule is split into two 3 carbon molecules (PGA -

stable). NADPH donates H+ to form 3 carbon phosphate molecule

(PGAL). Some 3 carbon phosphate molecules exit the cycle, join with

another 3 carbon phosphate molecule = hexose, which builds glucose.

Some 3 carbon phosphate molecules remain in the cycle to regenerate RuBP.

Light independent

Light independent

Light independent

Light independent

Light independent

Light independent

Light independent

Light dependentInputs OutputsNADPH (light dependent) NADPATP ADP + PiCO2 Glucose

Water

Factors affecting photosynthesis CO2 Light intensity Temperature Oxygen (reduces

carbon dioxide fixation)

Water (reduced water causes stomata to close, therefore less CO2 can come in)

Amount of chlorophyll.

Cellular Respiration

Cellular respiration is the process in which an organism breaks down an energy rich molecule (glucose) to release the energy in the usable form (ATP).

Aerobic respiration requires O2 (efficient)

Anaerobic respiration doesn’t require O2 (inefficient)

Aerobic Respiration Occurs in three stages Glycolysis - cytoplasm Kreb’s cycle – matrix of the

mitochondrion Electron Transport Chain – cristae of

the mitochondrion

Glycolysis Occurs in the cytoplasm.

Glucose enters

It is broken down into two pyruvate/pyruvic acid.

2 ATP molecules are produced

2 NADH molecules are produced

Doesn’t require O2

Glucose

Glycolysis

2 NADH

2 pyruvate (pyruvic acid)

2 ATP

In between Occurs in the matrix of the mitochondria. 2 pyruvate molecules (from glycolysis) enter the

mitochondrion. Pyruvate undergoes a reaction that results in the

formation of a compound called acetyl CoA. CO2 is produced as a by product of this reaction. Loaded NADH carriers are also created.

The reaction that occurs now is called the Krebs cycle.

2 pyruvate 2 Acetyl co A2 Carbon Dioxide 2 NADH

Kreb’s cycle Occurs in the

mitochondrial matrix

O2 required

Net yield of 2 ATP per glucose molecule (per 2 acetyl CoA)

Net yield of 6 NADH and 2 FADH2 (FAD serves the same purpose as NAD)

Electron Transport Chain Occurs in the cristae of the mitochondria Electrons are released from NADH and

from FADH2 and are passed along a series of enzymes.

Electrons are transported via cytochromes (series of compounds).

H+ ions are actively transported across the inner mitochondrial membrane.

The H+ ions then flow back through special pores in the membrane, a process that is thought to drive the process of ATP synthesis.

Net yield of 32 ATP per glucose molecule

6 H2O are formed when the electrons unite with O2 (electron acceptor) at the end of electron transport chain and then bind with 2H to form water.

Aerobic respiration in a nutshell

Anaerobic respiration

Putting it all together