Mutations - in depth

A mutation is change in the amount of or arrangement of the genetic material in the cell. They can be chromosomal mutations which involves changes to parts or whole chromosomes. Or, they can be DNA mutations which are changes to the nucleotide base sequences.

What causes mutations?

• During the process of replication, DNA is normally copied exactly so that the genetic material remains the same from generation to generation. However, occasionally changes can occur so that an organism may inherit altered DNA.
• The sudden change that can occur may produce an individual which is obviously different from the rest of the population. e.g. bacteria resistant to penicillin.
• Altered DNA molecules replicates the changed sequences so that the mutant genes are passed on to successive generations. - Such inherited changes are known as mutations.
• Mutation is another source of genetic variability n a population and it can occur spontaneously. 
• Mutant genes tend to be recessive but are transmitted in the normal way
• most mutations are harmful to the organism but some can be useful
• spontaneous mutations are essential for providing a new variation necessary for survival in a changing environment; in other words, it proves raw materials for evolutionary change
• The frequency with which one allele mutates to another is known as the mutation rate or mutation frequency and is measured by their occurrence in a population 
• mutations tend to be rare but the mutation rate can be speeded up by certain factors called mutagens or mutagentic agents which include x-rays, gamma rays and UV light which can damage DNA in various ways
• mutagens also include certain chemical substances which alter DNA by adding or deleting one or more bases in a sequences
• chemical mutagens include nitrous acid and 5-bromouracil

DNA mutations

• during protein synthesis, the sequence of ases in DNA is transcribed into a complementary sequence of bases in RNA which is then translated into a sequence of amino acids
• each sequence of three bases is a code for a specific amino acid, so that if the code is altered, this may result in an incorrect sequence of amino acids
• these changes would therefore result in non-functional proteins or proteins with a different function

Types of DNA mutations

• Point mutations - one base replaces another - also called substitutions
• Insertion/deletion mutations - one or more nucleotide pairs are inserted/deleted from a  length of DNA which causes frameshift
• A gene mutation in which a nucleotide is left out is called a deletion and a mutation in which a nucleotide is gained is called an insertion. 

• The effect on the sequence of amino acids from this small change in the DNA base is great.
• Every amino acid after the change ight be replaced by a different amino acid.
• both base deletion and base insertion have resulted in a shift so that all subsequent codons are altered.
• it is not surprising that mutation can result in the synthesis of a totally different protein

SICKLE CELL ANAEMIA

• The kind of point mutation that causes sickle cell anaemia is called substitution
• this is because the mutation is due to the substitution of one base for another just one place in the DNA molecule (thymine is replaced by adenine)
• the result of this is that the beta-chains of haemoglobin contains the amino acid valine at position 6 instead of glutamic acid
• Effect
• the haemoglobin is less soluble than normal haemoflobin and causes the RBC to become distorted into a sickle shape.
• this has many effects including severe anaemia and a clumping of cells which may lead to heart failure
• sickle-cell anaemia is often fatal before middle age

CYSTIC FIBROSIS

• 70% of the cases if cystic fibrosis the mutation is the deletion of a triplet base pair
• this deletes one amino acid out of a chain of 1480 in the normal polypeptide
• cystic fibrosis produces extra thick and very sticky mucus
• this can accumulate in the lungs and pathogens would normally be removed in the mucus by cilia  but the cilia are unable to move the mucus and thus causing infection - physiotherapy is required to get rid of it

ONCOGENES

• growth- promoting genes called protooncogenes
• these can be changed to oncogenes by point mutation so they cannot be turned off
• oncogenes promote unregulated cell division so this can lead to tumour. 

HUNTINGTON DISEASE

• Huntington disease results from an expanded triple nucleotide repeat
• the normal gene has a repeating CAG sequence above a certain threshold the protein alters sufficiently to cause the disease
• the symptoms are see later in life and include dementia and loss of motor control

Mutations w/ a neutral effect

• A change in the base sequence may produce no change in the organism if
• the mutation is a non-coding region of the DNA
• is a silent mutation - the change in the base does not alter the amino acid sequence
• the change in the organism is not seen as an advantage or disadvantage e.g. taste

Harmful/Beneficial effects:

• Early humans in Africa almost certainly had dark skin
• the pigment melanin protected them from the UV light
• they could however, still synthesise vit D from the action of intense sunlight on their skin
• humans with mutations resulting in paler skin would have been burned or suffered skin caner
• as humans migrated to more temperate areas sunlight was not intense enough to produce sufficient vit D by those with dark skins
• those with the pale mutations would have had an advantage (as a lack of vit D leads t rickets, narrow pelvis etc.)
• the Inuit peoples have not lost all their skin pigments although they dont live in an area with intense sunlight
• however, they eat a lot of vit D rich fish and seal meat.

AS Biology F212: Enzymes

Enzymes are proteins

• These are catalysts of biochemical reactions and speeds up these reactions so they occur at normal body conditions.
• All enzymes are globular proteins, therefore they are soluble.
• The molecule on which the enzyme acts is called the substrate.

Properties of enzymes

• They act as a catalyst
  They speed up a chemical reaction without being used up themselves
• They are high specific
  In general, one enzyme will only catalyse one particular reaction/substrate
• Enzymes are effective in small amounts
• The enzymes do not alter the nature of the products

Active site

• The active site is an area on the surface of the protein where the reaction occurs
• it has a very specific shape that is complementary to that of a substrate

Mechanism of enzyme action

• The enzyme and substrate combine to form a complex (the enzyme-substrate complex)
• The complex then break down to give products and release the enzyme for further use

Enzyme actions

Chemical reactions

• Particles in gases and solutions continually move about and will collide with each other.
• During a chemical reaction two reactants collide and combine to form an intermediate activated complex or transition state, which breaks down to form products.
• In all reactions a certain amount of energy is needed for the reactants to form the transition state
• This energy is known as the activation energy and without it chemical reactions cannot proceed
• The energy comes from maltose which can be boiled in acid - this provides the right conditions for maltose molecule to collide with water molecules energetically enough to hydrolyse

Activation energy

• Before a reaction can occur it must overcome an energy barrier by exceeding its activation energy
• Enzymes work by lowering this activation energy s that the reaction happens more readily
• Enzymes allow reactions to take place at lower temperatures (found in cells)

Lock & Key 

• This idea would explain why enzymes are specific
• The substrate (key) fits the shape of the enzyme (lock)
• Once the products have been made they no longer fit the active site and are released from the enzyme which can react with another substrate because its active site is available once more

Induced fit

• The lock and key model considers the enzyme to have rigid active site and a reaction would depend on the randomly moving substrate molecule entering the active sight in the right orientations
• This is unlikely to happen
• As the substrate collied with the active site - it changes the shape of the enzyme
• This allows the active site to fit more closely around the substrate
• Te substrate is held by the oppositely charged R-groups of the active site
• This is the enzyme-substrate complex
• The product is different shape to the substrate
• They do not fit the active site and are released
• The enzyme is free to catalyse further reactions

Enzymes and temperature

• Temperature and kinetic energy
• Molecules (liquid or gas) move around continually
• This random movement is due to kinetic energy
• Increasing temperature increase this energy
• This increases the frequency and force at which molecules collide
• Enzymes and kinetic energy
• Increased kinetic energy
• Increased number of collisions between active site and substrate
• Increased successful collisions = more enzyme substrate complexes
• Thus, increased rate of reaction
• Temperature
• Increasing temperature increases the rate of reaction up to the optimum temperature.
• Optimum temperature is the maximum rate of reaction
• After this rate of reactions begin to decrease
• Above the optimum the temperature rate of reaction decreases due to the breaking of the bonds that hold the enzymes tertiary structure in place
• This is caused by vibrations of the bonds
• The more that are broken the greater the chance the active site will change
• if this happens the enzyme wills top working - it can't function
• This irreversible change is called denaturation 
• Different enzymes have different optimum temperatures an therefore become denatured at different teoratures

Enzymes and pH

• pH is the measure of the Hydrogen ions concentration.
• pH7 is neutral, below is acidic and above is basic.
• The greater the concentration of hydrogen ions the more acidic it is.
• H+ are attracted to the negatively charged parts of molecules and repelled by positively charge parts.
• Proteins (enzymes) rely on interactions between positive and negative regions to maintain its 3D tertiary structure 
• The H+ can interfere with the hydrogen and ionic bonds which alters the tertiary structure - this causes a change in the shape of the active site then it will effect the rate of an enzyme controlled reaction
• Optimum pH
• This is the pH at which the rate of reaction is highest.
• Enzymes work in a fairly narrow range of pH.
• At this value the H+ concentration gives the tertiary structure its best shape
• The active site is most complementary to the substrate  
• An enzymes optimum pH will be related to the pH of the environment in which it is found
• e.g. Pepsin is a protein digesting enzymes found in the stomach and has an optimum pH of 2
• Trypsin is found in the small intestines which has a pH of 7

Effects of concentration

• No substrate = no enzyme-substrate complexes thus no reaction
• more substrate = more collisions = higher rate of reaction
• this continues until a maximum rate is reached =Vmax
• At this point all the active sites are occupied at any one point in time
• therefore increasing the substrate concentration has no further effect
• the enzymes concentration is a limiting factor
• Enzyme concentration increased > more active sites > more enzyme substrate complexes ? rate of reaction increases
• BUT, a point will be reached where all substrate molecules are occupying active sites
• the substrate is sad to be a limiting factor
• if the substrate is in excess (concentration is high) then the rate of reaction can increase
• the substrate is no longer a limiting factor

Initial reaction rate

• The highest rate of reaction will be seen when the enzyme and substrate are first mixed
• As tie asses the substrate concentration will decrease and thus the rate of reaction ill decrease
• The frequency of collisions will decrease
• The highest reaction rate is known as the initial rate

Inhibition

• Some substance can prevent or slow down the action of enzymes
• These are called inhibitors
• Inhibition can be competitive or non competitive 
• Competitive
• Have a similar structure to the substrate
• prevents the substrate from entering
• level on inhibition depends on the relative concentration of substrate and inhibitor
• this because the substrate and inhibitor are competing for active sites
• Non-competitive
• These do not compete for the active site
• they attach at the region away from the active site
• this changes the tertiary structure of the enzyme
• this causes the active site shape to change
• the substrate no longer fits
• enzyme substrate complex cannot form
• If there are enough inhibitor molecules present to bind to all the active site then the reaction will stop.
• Increasing the substrate concentration will have no effect
• Reversible and irreversible
• both competitive and non competitive enzymes can be reversible or irreversible
• this depends on the whether the inhibitor unbinds with the enzyme or not
• if it stays bound then it's irreversible inhibiton and the enzyme can no loner be used

Cofactors

• Non-protein substance needed for enzymes to catalyse a reaction
• e.g. coenzymes, prosthetic groups, inorganic ion cofactors. 
• Coenzymes
• small
• organic
• non-protein
• binds to active site
• takes part in the reaction and are changed like the substrate 
• can be recycled and used again
• Vitamin B3
• This helps the body break down carbohydrates and fats releasing energy
• Needed for the eznyme pryuvate dehydrogenase to function properly
• This is an enzyme needed n respiration
• A disease called pellagra results from absent from diet
• diarrhoea, dermatitis, dementia, death
• Prosthetic groups
• this is a coenzyme that is permanent part of an enzyme
• they contribute to the 3D shape and tare therefore vital to the function
• e.g. Carbonic anhydrase as a zinc based group
• Inorganic ion cofactors
• these can increase the reaction rate
• they combine with either the substrate or enzymes
• it makes the formation of enzyme substrate complex easier
• this is due to its affects the charge distribution and sometime shape of the eznyme

Interfering with enzymes

• Cystic fibrosis
• affects on respiratory system
• also blocks the passage of digestive enzymes produces by the pancreas into the gut
• leads to digestive difficulties
• tablets are prescribed containing enzymes packaged in an acid resistant coat
• Ethylene glycol poisoning
• this product is found in antifreeze
• it is not poisonous but when ingested it gets broken down in the liver
• carried out by the enzyme alcohol dehydrogenase
• this produces oxalic acid which is extremely toxic and can lead to death 
• treatment: large doses of ethanol is given which causes severe alcohol intoxication
• the ethanol is a competitive inhibitor of alcohol dehydrogenase
• Snake venom
• mixture of toxins and enzymes
• Phosphodiesterase interferes with the working of the preys heart
• the inhibitor of the enzyme acetyl cholinesterase - involved in nerve transmission = paralysis
• Antibiotics and bacterial resistance
• some bacteria are resistant to antibiotics because of the mutation in their DNA which results in them being able to produce enzymes that inactivate antibiotics
• many produce an enzyme (beta lactamase) that breaks down penicillin
• this resistance can be passed on when they replicate
• HIV treatment
• this is treated with chemicals that inhibit protease enzymes
• this prevents the virus from replicating
• they are often competitive inhibitors