Regulation of Transcription and Translation

Regulation of Transcription and Translation

The general principles involved in preventing expression of a gene by preventing transcription

1)      For transcription to begin the gene needs to be developed by a specific molecule that moves from the cytoplasm to nucleus.

2)      Each transcription factor has a site that binds to specific region of the DNA in the nucleus.

3)      When it binds, it stimulates the region of the DNA to begin the process if transcription.

4)      Messenger RNA is produced and the genetic code it carries is translated into a polypeptide.

5)      When a gene is not being expressed (switched off) the site on the transcription factor that binds to DAN is blocked by an inhibitor molecule

6)      This inhibitor molecule prevents the transcriptional factor binding to DNA and so prevents transcription and protein synthesis.

Hormones like oestrogen can switch on a gene and thus start transcription by combining with a receptor on the transcriptional factor.

This releases the inhibitor molecule.

1)      Oestrogen is a lipid soluble molecule and therefore easily diffuses through the phospholipid portion of the cell surface membrane

2)      Once inside the cytoplasm of a cell oestrogen combines with a site on the receptor molecule of the transcription factor.

The shape of this site and the shape of the oestrogen molecule complement one another.

3)      By combing with the site, oestrogen changes the shape of the receptor molecule. This change of shape releases the inhibitor molecule from the DNA binding site on the transcriptional factor.

4)      The transcriptional factor can now enter the nucleus through a nuclear pore and combine with DNA

5)      The combination of the transcription factor with DNA stimulates transcription of the gene that makes up the portion of DNA.

The effect of siRNA on gene expression

·         Gene expression can be prevented by breaking down messenger RNA before its genetic code can be translated into a polypeptide

·         Essential to the process of preventing gene expression is small double stranded sections of RNA called small interfering RNA or siRNA

1)      An enzyme cuts down large double-standard molecules of RNA into smaller sections called small interfering RNA – siRNA

2)      One of the two siRNA strands combine with an enzyme

3)      The siRNA molecule guides the enzymes to a messenger RNA molecule by pairing up its base with the complementary ones on a section of the mRNA molecule.

4)      Once on position the enzymes cuts the mRNA into smaller sections

5)      The mRNA is no longer capable of being translated onto a polypeptide.

6)      This means that the gene has not been expressed or in other words it has been blocked.

siRNA has a number of potential scientific and medical uses .

1)      It could be used to identify the role of genes in a biological pathway.

Some siRNA that blocks a particular gene could be added to cells

By observing the effects or rather the lack of them we could determine what the role of the blocked gene is.

2)      As some diseases are genetic (caused by genes ) it may be possible to use siRNA to block these genes and thus prevent the disease.  

Anaerobic respiration

Anaerobic respiration- Notes

·         In the absence of oxygen, the link reaction, kerbs cycle and electron transport chain could not take place

·         This leaves only the anaerobic process of Glycolysis as a potential source if ATP

However !

·         For Glycolysis to continue, its products; pyruvate and hydrogen must be released in order for NAD to be regenerated. If there is no none reduced NAD then glycolysis cannot take place.

·         NAD is replenished by pyruvate accepting the hydrogen from the reduced NAD

The Products

·         In eukaryotic cells and in some microorganisms such as yeast, the pyruvate is converted to ethanol and carbon dioxide.

Pyruvate + reduced NAD --> ethanol + carbon dioxide + NAD

·         In animal cells, the pyruvate is converted lactic acid.

Pyruvate + reduced NAD --> Lactate + NAD

Energy Yields From Anaerobic and Aerobic Respiration

In respiration energy is derived in two ways

1.       Substrate level phosphorylation

This happens in glycolysis and the krebs cycle and is the result of ADP reacting with inorganic phosphate to from ATP directly.

2.       Oxidative Phosphorylation

This happens during the electron transport chain. Oxidative phosphorylation is the indirect linking of ADP and inorganic phosphate . The energy yield for this is much greater than it is for this type of phosphorylation 

Bit of Chemistry- Enthalpy Change Definitions

Enthalpy Change Definitions

Enthalpy of Formation  

The standard molar enthalpy of formation, is the enthalpy change when one mole of a compound is formed from its constituent elements under standard conditions with all reactants and products in their standard states.

The Enthalpy of Atomisation

The standard enthalpy change of atomisation, is the enthalpy change which accompanies the formation of one mole of gaseous atoms from the element in its standard state, with the reaction taking place under standard conditions.

First Ionisation Energy

The first ionisation energy is the standard enthalpy change when one mole of gaseous atoms is converted into a mole of gaseous ions each with a single positive charge.

The second ionisation energy refers to the loss of a mole of electrons from a mole of single positively charged ions.

The First Electron Affinity

The fist electron affinity is the standard enthalpy change when one mole of gaseous atoms is converted to a mole of gaseous ions, each with a single negative charge.

 The Second Electron Affinity

The second electron affinity, is the enthalpy change when one mole of electrons is added to a mole of gaseous ions each with a single negative charge to from ions each with two negative charges.

Lattice Formation of Enthalpy

The lattice formation enthalpy, is the standard enthalpy change when one mole of solid ionic compound is formed from its gaseous ions

Enthalpy of Hydration

The enthalpy of hydration, is the standard enthalpy change when water molecules surround one mole of gaseous ions.

Enthalpy of solution

The enthalpy of solution, is the standard enthalpy change when one mole of solute dissolves completely in sufficient solvent to from a solution in which the molecules or ions are far enough apart not to interact

Mean Bond Enthalpy

The enthalpy change when one mole of gaseous molecules each breaks a covalent bond to from two free radicals, averaged over a range of compounds. 

Electron Transport Chain

Electron Transport Chain

Remember from earlier the products produced

·         Reduced NAD

·         Reduced FAD

Both of these are co-enzymes.                

The electron transport chain is the mechanism by which the energy from electrons within the  hydrogen atoms is converted into a form that the cells can us, namely ATP

The Electron Transport Chain and Mitochondria

Attached to the inner folds of the mitochondria membrane or cristae are the enzymes and other proteins involved in the electron transport chain and hence is the site of ATP synthesis.  

The Electron Transport Chain and Mitochondria

1.       The Hydrogen atoms produced during Glycolysis and the kerbs cycle combine with the coenzymes NAD and FAD to form reduced versions of themselves

2.       The Reduced NAD and FAD donate the electrons of the hydrogen molecules that they are carrying to the first molecule of the electron transport chain.

3.       This releases the protons from the hydrogen atoms which are then actively transported across the inner mitochondrial membrane

4.       The electron meanwhile is passed along a chain of electron transport carrier molecule in a series of oxidation-reduction reactions. As the electrons are passed down they release energy which is used to combine ADP and Pi to make ATP  

5.       The protons accumulate in the space between the mitochondrial membranes before they diffuse back into the mitochondrial matrix through specific protein channels.

6.       At the end of the chain the electrons combine with these protons and oxygen to form water.

This means that oxygen is therefore the final acceptor of electrons in the electron transport chains.

Remember that there are 3 different molecules that carry the electrons in the electron transport chain before oxygen finally accepts it electrons.

Oxygen is Important !

Without it the final hydrogen carrier cannot be removed from the end of the electron transport chain. If this did not happen then the electrons would back up  along the chain and the process of aerobic respiration would stop.

Cyanide

Cyanide is a non-competitive inhibitor for the final enzyme in the electron transport chain. This is the enzyme that catalyses the addition of hydrogen ions and electrons to oxygen to from water

As a result respiration cannot occur. 

Link Reaction and Krebs Cycle

Link Reaction and Krebs Cycle

Where ?

Both reactions take place in the matrix of the mitochondria.

The Process

·         Pyruvate is oxidised by NAD which removes a hydrogen to from reduced NAD (this is later used to produce ATP in the electron transport chain).

·         A 2-carbon acetyl group combines with a molecule known as co-enzyme A to from Acetyl co-enzyme A.

·         A carbon dioxide molecule is formed from each pyruvate

The basic word equation is :

Pyruvate + NAD + CoA --> Acetyl CoA + reduced NAD + Carbon Dioxide

Note CoA stands for Co-enzyme A

The Krebs Cycle

The Krebs cycle is a series of oxidation reduction reactions that take place inside the matrix of the mitochondrion.

1.      The 2-Carbon Acetyl- coenzyme A from the Link reaction combines with a 4 carbon molecule to produce a 6 carbon molecule.

2.      This 6 carbon molecule loses two carbon dioxides and hydrogen's to from a 4 carbon molecule. A single ATP molecule is produced as a result of substrate level Phosphorylation

3.      The 4 carbon molecule can now re combine with Acetyl-coenzyme A to start the cycle again (by producing the 6 carbon molecule again)

For 1 pyruvate molecule the link reaction and kerbs cycle produce

·         3 molecules of carbon dioxide

·         One molecule of ATP

·         Reduced NAD

·         Reduced FAD

Note that these molecules are given off when the 6-carbon molecule is broken down to the 4 carbon molecule.

Coenzymes

In respiration and photosynthesis, hydrogen atoms are carried by coenzymes from one molecules to another. They include :

1.      NAD

2.      FAD- Krebs cycle

3.      NADP - Photosynthesis

Significance of the Krebs Cycle

The Krebs Cycle is important for 4 reasons

1.      It breaks macromolecules down into smaller ones. For example Pyruvate is broken down to carbon dioxide.

2.      It regenerates the 4- carbon molecule that combines with acetyl-coenzyme A.

3.      It produces Hydrogen atoms that are carried by NAD to the electron transport chain.

4.      It is a source of intermediate compounds used by cells in the manufacture of other important substances such as fatty acids, amino acids and chlorophyll. 

Respiration- Glycolysis

Respiration- Glycolysis

·         Glycolysis is the initial stage of both aerobic and anaerobic respiration.

·          It occurs in the cytoplasm of all living cells.

·          It is the process by which a hexose sugar usually glucose is split into two carbon-3 molecules called pyruvate.  

The Process

1.       The activation of glucose by Phosphorylation

Glucose by itself is not reactive enough to be split. It must be made more reactive and this is done by its bonding to two phosphate molecules that come from the breakdown of ATP (that then becomes ADP)

2.       Splitting of the phosphorylated Glucose

Each glucose is split into two triose phosphate molecules.

3.       Oxidation of Triose phosphate

Hydrogen is removed from each triose phosphate molecules and is transferred to a hydrogen carrier molecule known as NAD to form reduced NAD

4.       The production of ATP

Enzyme controlled reactions convert each triose phosphate molecules into the 3-cardon molecule pyruvate .

Glucose --> 2 Triose Phosphate --(enzymes )--> 2Pyruvate

Energy Yield From Glycolysis

This is the yield for one glucose molecule.

Produced are :

2 molecules of ATP

4 molecules are produced but then two are used up in the Phosphorylation of glucose.

Two molecules of reduced NAD

Which are used later during the electron transport chain.

Two molecules of pyruvate

Which then go to the link reaction in aerobic respiration and help oxidise NAD in anaerobic respiration.   

Transmission of Nerve Impulses

Transmission of Nerve Impulses

Notes:

·         Neurones transmit impulses as a series of electrical signals

·         The electrical signals pass along the cell surface membrane surrounding the axon as a nerve impulse

Resting Potential 

In a resting axon the inside of the membrane has a negative electrical potential compared to the outside. This typically has a value of -70mV (this is the difference in charge between the Inside and outside of the axon membrane). The resting state of the axon is said to be polarised.

How is the resting potential produced and how is it maintained?

·         Neurons can maintain an internal composition which is different from that of the outside the neuron.

·         Na+ and K+ ions are transported across the membrane against their electrochemical gradient by active transport.

·         Carrier proteins in the membrane pick up the Na+ ions and transport them outside of the membrane

·         At the same time K+ ions are picked up and transported across the membrane into the axon.

·         This is known as the sodium potassium pump and it realise on ATP from respiration. The pump, pumps 3 sodium ions out of the axon while pumping only two potassium ions into the axon.

Remember

Outside = High Na+ concentration - Low K+ concentration

Inside = Low Na+ concentration High K+ concentration

 Why is the Outside Positive Compared to the inside?

·         Na+ ions are pumped out faster than K+ ions are brought back in.

·         K+ ions can diffuse out quicker than Na+ ions can be brought back in.

·         The net result is that the outside of the membrane is positive compared to the inside

·         The resting potential is established and the axon is said to be polarised

There are two gradients established across the axon membrane

1.      A concentration gradient

2.      A electrochemical gradient

3.      Action Potential

Notes

·         A nerve impulse can be initiated in a neurone by mechanical, chemical, thermal or electrical stimulations

·         When this happens the resting potential changes. It goes from around -70mV inside the membrane to +40

·         For a brief period of time, the inside of the axon becomes positive and the outside becomes negative.

·         This change on the potential is called the action potential and lasts for around 3ms

When an action potential occurs, the axon is said to be depolarised.

When the resting potential is re-established the axon membrane is said to be repolarised.

Depolarisation- How does it occur?

1.      The axon membrane changes its permeability to Na+ and K+ ions

2.      When the axon is stimulated, Na+ channels open in the membrane. Na+ ions move into the axon by diffusion down an electrochemical gradient.

3.      The influx of Na+ ions create a positive charge of +40mV inside the axon membrane

4.      K+ channels open and K+ ions diffuse out along their electrochemical gradients which starts of repolarisation

5.        At the same time sodium channels close so that Na+ ions can no longer enter

The resulting potential is re-established, the outside becomes positive and the inside becomes negative again

The membrane is said to have become repolarised.

In fact so many K+ ions leave that the inside becomes more negative than it was originally.The membrane is said to be hyperpolarised. 
K+ channels eventually close and the sodium potassium pump starts again . This restores the normal concentration of Na+ and K+ ions either side of the membrane, this re-establishes the resting potential  

Control by Chemoreceptors

The Control of Heart Rate

Heart rate is controlled by the autonomic nervous system.

Autonomic means self-governing, the autonomic nervous system controls the involuntary (or subconscious) workings of the internal muscles and glands.

It divides into two: 

1.       The sympathetic Nervous System

Used to help us cope with stressful situations by heightening our awareness and preparing us for activity

2.       The Parasympathetic Nervous System

In general, this inhibits effectors and slows down any activity. The parasympathetic nervous system also controls activities under normal resting conditions and its purpose is to conserve energy and to replenish the body’s reserves.

These systems are often antagonistic. If one system contracts a muscle, then the other relaxes it. Our internal glands and muscles are therefore regulated by a balance of the two systems.

One such example is heart rate:

·         The resting heart rate of an average human being is around 70 beats per minute

·         During exercise the resting heart rate may need to more than double to supply the active tissue with oxygen and food.

Changes to the heart rate are controlled by the Medulla Oblongata a region of the brain which has two centres.

1)      The first decreases heart rate- Parasympathetic Nervous System 

2)      The second that increases heart rate – Parasympathetic Nervous System

Both of these centres and linked to the Sino atrial node by their various nervous systems

The site that is stimulated depends upon the stimuli received by the receptor. In the case of heart rate it could be either

1)      Chemical changes in the blood, detected by chemoreceptors

2)      Pressure changes in the blood detected by Baroreceptors

Control by Chemoreceptors

·         Chemoreceptors detect chemical changes and are found in the walls of the carotid arteries which serve the brain.

·         These chemoreceptors are sensitive to changes in the pH of the blood that result from the changes in carbon dioxide concentration changes.

The process works as follows

1)      When pH falls the chemoreceptors in the walls of the carotid arteries and aorta detect this and increase the frequency at which they send nervous impulses to the centre in the medulla oblongata that is responsible for increasing heart rate.

2)      Via the sympathetic nervous system, the medulla oblongata in turn increases the rate at which it send nervous impulses to the Sino atrial node.

3)      The Sino atrial node as a result increases the rate at which it causes the muscles of the heart to contract.

4)      This means that the blood travels around the body faster and thus more carbon dioxide is removed from the blood by the lungs.

5)      With less carbon dioxide in the blood the pH returns to its normal value.

6)      This rise in pH is detected by the carotid arteries and they reduce the frequency at which they send impulses to the medulla oblongata causing the heart rate to return to normal.

Control by the pressure receptors

These receptors are also found in the carotid arteries and walls of the aorta.

They operate much the same as the chemoreceptors

1)      A higher than normal blood pressure is detected by the pressure receptors

2)      Nervous impulses are transmitted to the centre in the medulla oblongata

3)      The medulla oblongata in turn decreases the rate at which it sends nervous impulses to the Sino atrial node via the parasympathetic nervous system.

4)      The Sino atrial node stops the heart beating as fast or as powerful

5)      Blood pressure falls.

Translation

Translation

Translation is the process by which the information on mRNA is used by the tRNA to synthesise a polypeptide chain which will eventually form a protein. The formation of proteins happens in the ribosomes which can be situated freely in the cytoplasm or just attached/part of the rough endoplasmic reticulum. The proteins which as synthesised freely in the cytoplasm are used by the cell for its various functions, the protein synthesised by the ribosomes on the rough endoplasmic reticulum often go to the Gogli apparatus before being released by the cells into the surroundings.

The ribosomes ‘read’ the genetic message on the mRNA while the tRNA delivers the amino acids in the sequence originally determined by the template strand of the DNA.

Remember

The structure of tRNA

·         The anti-codon is complementary to the nucleotides on the mRNA strand and the acceptor strand is complementary to the relevant amino acid.

The Structure/Role

·         To pick up amino acids from the cytoplasm and to transfer them to the ribosomes in the correct sequence.

The Process

1.       The codons on the mRNA move the ribosomes from the nucleus out of the nuclear pores in the nuclear envelope.

2.       tRNA collects the complementary anti-codon triplet which is situated on the mRNA strand.

3.       The amino acid is put into the right place in the chain.

4.       The amino acid bonds to the forming polypeptide chain while the tRNA is released.

5.       The process is repeated until the whole of the mRNA chain has been translated

The correct sequence from the original DNA has been transferred and a polypeptide chain has been made.

In the Ribosomes on the rough endoplasmic reticulum after translation the proteins pass into the cisternae of the golgi. Vesicles are formed containing the proteins in a concentrated form with the possible addition of carbohydrates. The vesicles break off abd move to the cell membrane, the vesicles then fuse with the cell membrane and are carried through the membrane to be secreted into the surrounding environment.  

Genes and Gene Expression

Genes and Gene Expression

Ribonucleic acid  RNA

RNA unlike DNA forms a single strand in which nucleotides make up.

Each nucleotide is made of:

·         The pentose sugar ribose

·         An organic base Adenine (A) , Guanine (G) Cytosine (C) and Uracil (U)

·         A phosphate group

·         There are two types of organic bases; purines and pyrimidines.

·         Purines are made up of Hexagonal and Pentagonal rings, Adenine and Guanine are purines.

·         Pyrimidines are made up of a single Hexagonal ring and consist of Thymine, Cytosine and Uracil.

·         Remember form AS - Guanine with Cytosine and Adenine with Uracil (RNA) or Thymine (DNA)

Transcription= DNA à RNA

Translation = RNA à Protein

Therefore DNAà RNA àProtein

There are two types of RNA that are important in protein synthesis, they are

·         Messenger RNA (mRNA)

·         Transfer RNA

Important Note!

·         When we talk about a triplet code or a codon we are talking about messenger RNA

·         In RNA there is no Thymine but rather it is replaced by Uracil

Messenger RNA (mRNA)

·         mRNA is a long strand that is arranged in a single helix

·         mRNA leaves the nucleus via pores in the nuclear envelope and enters the cytoplasm where it comes into contact with the genetic code.

Transfer RNA (tRNA)

·         tRNA is a smaller molecule but is still made up of a single strand.

·         The single strand is folded into a clover-leaf shape where one end of the strand extends beyond the other.

This extended section is that which an amino acid can be attached to.

·         At the opposite end of the tRNA there is an anticodon. The anticodon is made up of three other bases.

·         For each amino acid there is a different sequence of organic bases on the anticodon.

During protein synthesis the anticodon pairs with the three complementary bases that make up the triplet bases (codon) on mRNA. The structure of tRNA means that is structurally suited to its role in lining up amino acids on the mRNA template during the protein synthesis.

·         The end chain is for attaching amino acids

·         The anticodon is for pairing with the codons of mRNA