Protein synthesis and its regulation

Nucleotide:

The base present in a DNA nucleotide is either a purine or pyrimidine

Purines: Guanine and Adenine

Pyrimidines: Thymine and Cytosine 

1 purine pairs with 1 pyrimidine. Purine is bigger

Nucleotides can join together by condensation between the phosphate of one nucleotide and the deoxyribose of another. What type of bonds are formed when this happens: Covalent (phosphodiester bonds)

Bonds between bases = hydrogen bonds

Name of the molecule produced by the polymerisation of nucleotides: polynucleotides

Enzyme that is responsible for the polymerisation of nucleotides in a DNA molecule: helicase

Diagram:

In a molecule of DNA, there are 2 polynucleotide chains running in the opposite direction to each other.

Gene: A specific sequence of bases/nucleotides in DNA that codes for a polypeptide.

The bases on opposite strands are arranged to form complementary base pairs. A purine is always paired with a pyrimidine.

Adenine pairs with Thymine (2 hydrogen bonds between A & T)

Guanine pairs with Cytosine  (3 hydrogen bonds between G & C)

The complementary base pairs are held together by hydrogen bonds

The DNA molecule is twisted into a DOUBLE HELIX

The sequence of bases in DNA codes for the sequence of amino acids in a polypeptide chain. (polypeptide chain = lots of amino acids joined together). 3 bases code for 1 amino acid = triplet code

The genetic code has a number of features:

•  A sequence of 3 bases in DNA codes for 1 amino acid. The genetic codde is described as being a triplet code.
• Some amino acids can be coded for by more than one triplet of bases. The genetic code is described as being DEGENERATE.
• Any 1 base can only be part of 1 triplet. The genetic code is described as being NON-OVERLAPPING.
• Any given triplet specifies the same amino acid in all organisms. The genetic code is described as being UNIVERSAL.

The DNA of a eukaryotic organism is stored in the nucleus, but protein synthesis occurs on RIBOSOMES found in the cytoplasm and rough ER.

This means that the genetic code on the DNA must be transferred from the nucleus to the cytoplasm in some way. Sections of DNA that code for polypeptides are copied onto SINGLE stranded molecule known as RNA (Ribonucleic acid)

RNA

• RNA is a ribonucleic acid.
• Single stranded polynucleotide made up of RNA nucleotides
• These nucleotides have 3 components: pentose (5C sugar called RIBOSE); A nitrogenous base (A,T,G, U - URACIL) U replaces T. and also a PHOSPHATE group.

Diagram of RNA nucleotide:

Thymine NOT found in RNA

Uracile is a PYRIMIDINE

There are 2 types of RNA important in protein synthesis:

• Message RNA (mRNA)
• Transfer RNA (tRNA)

• Messenger RNA molecules may consist of 1000's of nucleotides in a SINGLE LINEAR STRAND.
• mRNA is formed by TRANSCRIPTION of a gene in DNA in the nucleus.
• It is complementary to the DNA in its base sequence.
• An amino acid is coded for by a TRIPLET of bases on mRNA called a CODON.
• mRNA has unpaired bases and so is easily broken down in the cytoplasm; it only needs to exist temporarily until the protein is manufactured.
• If there's 4 possible bases coding as a triplet, there's 64 possible codons (4 x 4 x 4)
• 3 bases on RNA = codons - which determine the sequence of amino acids which code for a protein.
• mRNA leaves the nucleus from nuclear pores and in cytoplasm is codes with ribosomes and is read.

tRNA brings amino acids to mRNA

• Transfer RNA is a relatively small molecule that is made up of around 80 nucleotides
• It is a SINGLE STRAND WHICH FOLDS BACK ON ITSELF.
• The tRNA molecule FORMS HYDROGEN BONDS WITHIN COMPLEMENTARY SECTIONS OF THE MOLECULE.
• These help to stabilise the molecules.
• One end of the chain attaches to an amino acid.
• There are several types of tRNA, rach able to carry a SINGLE SPECIFIC AMINO ACID.
• At the base of the tRNA molecule is a sequence of 3 bases, known as the ANTICODON.
• For each amino acid carried there is a different sequence of bases on the anticodon of tRNA
• Condon and anticodon are complementary to each other.

The bases in DNA pair up in a precise way (A & T + G & C) - these are known as complementary base pairs.

In RNA, Thymine is always replaced by a similar base called URACIL.

RNA can link with both DNA and other RNA molecules.

The complementarybase pairings that RNA forms are therefore: G & C + A & T (in DNA) or A & U (in RNA)

DNA

• double nucleotide chain
• largest molecule of the 3
• double helix shape
• penstose sugar is deoxyribose
• A,T,G,C
• found in nucleus of cell
• chemically stable

mRNA

• single nucleotide chain
• smaller than DNA, bigger than tRNA
• single linear strand
• pentose sugar is ribose
• A,U,C,G
• found in nucleus and cytoplasm
• less stable than DNA and tRNA

single polynucleotide chain

smallest molecule of the 3

single strand folded back on itself. forms H bonds within complementary sections of the molecule

pentose sugar is ribose

A,U,G,C

found in cytoplasm of cell

more stable than mRNA, less stable than DNA

Proteins are made up of polypeptide chains. 

• The DNA in the nucleus contains the instructions to make all the organisms proteins.
• Which proteins are manufactured depends upon the activities of the particular cell: eg beta cells in the pancreas make the protein hormone insulin.
• The genes to make some proteins may be switched off so the cell never produces that proteinL eg cells of the liver never make insulin.

Overview of protein synthesis:

• TRANSCRIPTION takes place in the nucleus of the cell and involves the formation of a precurosr RNA called pre-mRNA, that is a complementary sequence of bases to the DNA.
• RNA processing takes place in the nucleus so that non-functioning sequences of bases are SPLICED from the pre-mRNA to form mRNA. The mRNA then leaves the nucleus and attaches to a ribsome. 
• TRANSLATION which occurs on ribosomes, involves the translation of the mRNA message into a specific sequence of amino acids to form a polypeptide.

DNA -> mRNA -> Protein/polypeptide chain

Only 1 strand is involved. (PG 9)

Transcription is the process of making pre-mRNA using part of the DNA as a TEMPLATE

A portion of the gene to be transcribed is represented here as the separate strands of DNA with their bases exposed. The 2 DNA strands are separated by the enzyme DNA helicase (unzips)

ONE strand of  the DNA acts as the template upon which pre-mRNA is built - this TEMPLATE STRAND is sometimes referred to as the DNA sense strand. The RNA nucleotides are found in the nucleoplasm. The nucleotides line up against the DNA template by COMPLEMENTARY BASE PAIRING. 

Sense strand = copied strand. Antisense strand = not copied

RNA Polymerase : Joins strands back up. Catalyses formation of bonds between nucleotides.

Moves along sense strand, causing the nucleotides on this strand to complementary base pair with the individual free RNA nucleotides present in the nucleus. Joins up RNA nucleotides to make RNA polynucleotide.

The nucleotides bond together to form a pre-mRNA molecule carrying a sequence of bases that is complementary to that on the sense strand of the DNA molecule. 

SPLICING OF PRE- mRNA

• DNA is made up of sections called EXONS that code for the amino acid sequence of polypeptides and sections called INTRONS that do not.
• EXONS are sections of DNA that are EXPRESSED to produce proteins and INTRONS are intervening sequences of junk DNA, the function of which is not fully understood.
• In the pre-mRNA in EUKARYOTIC CELLS the introns are removed by enzymes and other molecules before the mRNA moves into the cytoplasm. 
• The remaining exons are joined together in a number of different combinations. This is known as SPLICING.
• Following splicing, mRNA molecules leave the nucleus through the nuclear pores.

Gene made up of 756 base pairs, the mRNA transcribed from this gene is only 524 nucleotides long. why?: Introns removed. pre-mRNA is spliced to remove introns and leave only coding exons which are used for translation.

This CODON DICTIONARY shows the amino acid coded for by each mRNA codon. (pg 11)

3rd base is least important

there are 3 particularly important things that should be noticed about the code:

• Often it is only the 1st 2 bases of the triplet that are specific for a particular amino acid (these 2 are most important), and any 3rd base will do. This also reduces the chance that a change in the bases will alter the function of the polypeptide.
• There are 3 STOP CODES. These indicate the END of a section of mRNA, after which point translation stops. UAA stop codon.
• The code for methionine, AUG, is used as a start code. This means that polypeptides normally start with a methionine group when they are freshly translated. It is often removed in the processing stage that converts the polypeptide into a functional protein. 

AUG - START = FIRST CODON

• Each ribosome consists of a large and small subunit and the process of translation begins when the 2 subunits bind to the start codon on mRNA, AUG. The ribosome is large enough to fit 2 tRNA molecules at any one time.
• The specific tRNA molecule with a anticodon UAC base pairs with the start codon and this carries the amino acid methionine. 
• In this example, a second tRNA with the anticodon CGG base pairs with the second mRNA codon G,C,C and is carrying the amino acid alanine. Alanine then forms a PEPTIDE bond with methionine to start the polypeptide chain.
• The 'empty' tRNA now moves away from the ribosome and can pick up another molecule of the same amino acid, methionine, from the cytoplasm. The ribsome then moves on to the next codon.
• A tRNA molecule with the anticodon U,G,A and carrying the amino acid A,C,U, is attracted to the complementary sequence of bases. Threonine on the mRNA.
• This process is repeated until the ribosome comes to a STOP codon on the mRNA. This signal the completion of the polypeptide chain and chain leaves the ribsome. 
• The mRNA codon UAA is a stop codon and thus no further tRNA molecules will attach to it. the tRNA and its polypeptide chain detach from the ribosome.
• The polypeptide chain is now free in the cytoplasm where it bends and folds into its final tertiary structure. 
• As more than one protein molecule is usually required by a cell at a time, then it is usual for a group of ribosomes to pass along the mRNA molecule each leading to the production of a completed polypeptide chain. Such a group of ribosomes is termed a POLYSOME.

Transcription - mRna is made

Regulation of transcription (happens in nucleus)

For transcription to begin the gene needs to be stimulated by specific proteins that move from the cytoplasm into the nucleus. These molecules are called TRANSCRIPTIONAL FACTORS (contain sites that bind to DNA)

The general process involved is:

• each transcriptional factor has a site that binds to a specific region of the DNA in the nucleus. This is known as the PROMOTER REGION (is on the DNA)
• binding of the transcriptional factor to the promoter region allows the attachment of RNA polymerase to the DNA and transcription begins
• Messenger RNA (mRNA) is produced and the genetic code it carries is then translated into a polypeptide

Transcriptional factors bind to DN on promoter region -> Attachment of RNA polymerase to DNA -> Transcription begins -> mRNA produced

When a gene is not being expressed (i.e. is switched off), the site on the transcriptional factor that binds to DNA is blocked by an INHIBITOR molecule. This inhibitor molecule prevents the transcriptional factor binding to DNA and so prevents transcrption and polypeptide synthesis.

Oestrogen is a lipid soluble, steroid hormone. It is transported in the blood stream and can reach almost any cell in the body. However it only binds to cells that have special oestrogen receptors. The binding of oestrogen to its receptor molecule is similar to that between a substrate and an enzyme. ie they have a complementary shape. 

Oestrogen receptor is inside the cell.

Oestrogen goes in between phospholipid molecule into cell then binds to receptor sites inside cell. These are TF.

Hormones like oestrogen can 'switch on' or activate a gene and thus start transcrption by combining with a receptor on the transcriptional factor. This releases the inhibitor molecule. (pg 15)

1) Oestrogen, like all steroid hormones, is a lipid, so crosses the cell membrane by lipid diffusion and enters the cytoplasm.

2) Oestrogen binds to its receptor in the cytoplasm (to form a hormone receptor complex). The oestrogen receptor acts as a transcriptional factor, and binding of oestrogen activates it (removes inhibitor).

3) The activated transcription factor diffuses into the nucleus through a nuclear pore.

4) In the nucleus the transcription factor binds to a specific base sequence in a DNA promoter region.

5) This binding stimulates RNA polymerase to transcribe a gene to stimulate protein synthesis (ie it allows the gene to be expressed)

Oestrogen binds to transcriptional factors and changes its tertiary structure/shape so inhibitor molecules released -> TF can now bind to DNA as site is exposed -> Polymerase binds -> Transcription occurs.

Inhibitor molecule prevents TF binding to promoter region

Small interfering RNA (siRNA) stops MRNA being translated into a protein

Works on excess RNA and so regulates it

It also chops up mRNA -> so inhibits translation

In the cytoplasm there are small double stranded sections of RNA called small interfering RNA. they are key to a process called RNA interference which is the inhibition of gene expression at the translation stage.

This will be important in a cell when: if mRNA concentration is regulated, it will limit the amount of protein translated (ie prevents excess protein being made and can prevent expression of viral proteins)

The siRNA binds to a protein called RISC. RISC breaks the double stranded siRNA into its separate strands. 1 strand stays attached to RISC and other discarded so attaches to mRNA. 

• siRNA is made by special regulatory genes
• it moves into the cytoplasm and becomes single stranded
• it binds to specific mRNA molecules by complementary base pairing
• this cuts the mRNA in 2
• the mRNA can no longer be translated so protein synthesis stops

applications of siRNA in scientific research

siRNA with specific sequences can be synthesised and used to silence specific genes making them valuable toools in both research & medicine:

• It could be used to identify the role of genes in a biological pathway. Some siRNA that blocks a particlar gene could be added to cells. By observing the effects (or lack of them) we could determine what the role of the blocked gene is
• As some diseases are caused by genes, it may be possible to use siRNA to block these genes and so prevent the disease

This occurs when there is a change in the sequence of nucleotide bases in DNA. Gene mutations generally occur through 1 of 2 processes:

1. Spontaneous mutations when a cell replicates its DNA in prep for cell division. mutations result when the DNA polymerase makes a mistake

2. DNA damage from mutagenic agents which increase the rate of mutation (e.g. chemicals from tobacco smoke, x rays, uv light)

the change in the genetic code caused by a mutation may result in:

• a different amino acid sequence in the encoded polypeptide (protein). this protein may not have the same tertiary structure as the original, and often does not work in the same way. a mutation can produce a different form of the gene - a new alllele
• no change in the amino acid sequence in the encoded polypeptide. this may arise as a result of the genetic code being dengerate. and a mutation may result in a different triplet code which codes for the amino acid acid as the orginal amino acid

Substitution

the type of gene mutation in which a nucleotide in a DNA molecule is replaced by another nucleotide that has a different base is known as substitution.

Depending on which new base is substituted for the original base, there are 3 possible consequences:

• non-sense mutation occurs if the base change results in the formation of a stop codom that makrs the end of translation. as a result the production of the polypeptide would be stopped prematurely. the final protein would amonst certainly have a altered tertiary structure so would be non functional. (Stops translation so only part of polypeptide chain produced)
• mis-sense mutation arises when the base change results in a different amino acid being coded for. the polypeptide produced will differ in a single amino acid. the significance of this difference will depend upon the precise role of the original amino acid. if it is important in forming bonds that determine the tertiary structure of the final protein, then the replacement amino acid may not form the same bonds. the protein may then be a different shape and not function properly.
• a silent mutation occurs when the substituted base, although different, codes for the same amino acid as before. this is due to the degenerate nature of the genetic code, in which most amino acids have more than 1 codon. there is no change in the polypeptide produced and so the mutation has no effect.

Deletion

a gene mutation by deletion arises when one or more nucleotides are lost from the normal DNA sequence. usually the amino acid sequence of the polypeptide is entirely different

this is because the genetic code is a triplet one. it is read in units of 3 bases. one deleted nucleotide creates what is known as a "frameshift" because the reading frame that contains each 3 letters of the code has been shifted to the left by one letter. the gene is now read in the wrong 3 base groups and the genetic message is altered.

one deleted base at the very start of the sequence could alter every triplet in the sequence. a deleted base near the end of the sequence is likely to have a smaller impact but can still have consequences.

All of this and the previous flashcard, happens during DNA replication

Mutations can ause genetic disorders and some cancers

• if the mutation is acquired (occurs after fertilisation) they can cause cancer
• if the mutation is hereditary, i.e. in the gametes, it can cause genetic disorders as well as some cancers

acquired mutations and cancer

cell division is controlled by genes. most cells divide at a fairly constant rate to ensure that dead/worn out cells are replaced. 2 types of genes play major roles in controlling the rate of cell division:

• proto-oncogenes that stimulate cell division & differentiation. it is involved in the control of mitosis. proto-oncogene is the normal gene, but due to mutation becomes oncogene
• tumour supressor genes that inhibit cell division

the presence of certain growth factors will activate a proto-oncogene and in this state it is permanently activated. oncogenes cause normal cells to divide too quickly and become cancer cells.

tumour suppressor genes are normally genes that inhibit cell division, when it is no longer necessary. when tumour supressor genes are mutated, they become inactivated allowing cells to divide uncontrollably. 

example of tumour supression gene mutation:

• an important tumour supressor protein is known as p53. this protein stops the cell cycle moving from g1 to s phase in mitosis.
• p53 protein is encoded by the p53 gene
• if the gene mutates, the p53 protein has a different tertiary structure and so is unable to halt the cell cycle so cells divide uncontrollably. this is cancer.
• mutated p53 genes are found in 70% colon cancers, 30-50% breast cancers and 50% lung cancers
• abnormalities of the p53 gene can also be inherited

• g1 = synthesis of amino acids and enzymes etc.
• s  = dna replication
• g2 = another growth phase
• m = mitosis

treatment and diagnosis of disorders caused by mutations

acquired mutations are caused by mutagenic agents

• prevention of the cancer may be possible by avoiding the mutagen, e.g. vaccination to prevent cervical cancer (caused by HPV virus), sunscreen to protect against UV, quit smoking
• diagnosis normally happens after symptoms have appeared. if someones at high risk they may be screened regularly. e.g. suffers from crohn's disease at high risk for colon cancer. earlier diagnosis increases chances of recovery. identifying if a specific gene has mutated, can make the identification of a particular type of cancer faster and more accurate
• treatment depends on the type of cancer; knowing if a cancer is fast or slow growing enables decisions to be made regarding the dose of radiation/chemottheraphy to be given

hereditary (inherited) are usually accompanied by family history of a certain type of cancer

• diagnosis may be via dna screening for particular genes followed by more frequent screening for a specific cancer, e.g. mammograms for breast cancer, colonscopies for colon cancer
• prevention may be limited to pre-emptive surgery, such as mastectomies to prevent breast cancer
• treatment is similar to that for cancers due to acquired mutation but early diagnosis may result in lower doses of radio or chemotheraphy

non cancerous genetic disorders caused by hereditary mutations

• can be diagnosed by DNA screening-this could be for all those with a family history, or in an embryo where the parents may wish to make decisions regarding termination, or to allow them to prepare for a child with a serious medical condition
• may be prevented by pre-implantation diagnosis during IVF although this also has ethical implications
• treatment of them will depend on the mutation - in the future, gene theraphy may be posible by inserting a healthy copy of the gene. other treatment may be dealing with symptoms associated with the specific conditions.

differentiated cells differ from each other because they produce differnt proteins. the proteins that a cell produces are coded by for the genes but not all genes are switched on, or expressed. this means that most cells can only divide to produce cells of the same type as themselves, as they can only translate some of their DNA.

However, stem cells, are capable of translating different parts of their DNA and so can form different types of cell when they divide (which type of cell they become depends on which genes are expressed)

there are 2 important types of stem cells:

• totipotent cells are cells that can mature into any body cell. in mammals, totipotent cells are found in embryos and occur only for a limited time. during development (i.e. when they divide) totipotent cells translate only part of their dna, resulting in cell specialisation.
• an organism develops from a single fertilised egg. a fertilised egg (zygote) clearly has the ability yo give rise to all types of cells. zygotes are therefore totipotent cells. the early cells that are dervied from the zygote are also totipotent. these later differentiate and become specialised for a particular function.
• multipotent cells are found in mature mammals. these can divide to form only a limited number of different cell types. 

Unlike mammalian cells, mature plants have many totipotent cells. under the correct conditions, many plant cells can develop into any other cells

for example, if we take a cell from the root of a carrot, place it in a suitable nutrient medium and give it a certain chemical stimuli at the right time, we can develop a complete new carrot plant. growing cells outside of a living organism in this way is called in vitro development

since the new carrot plant is genetically identical to the one from which the single root cell came from, it is a clone. cells from most plant species can be used to clone new plants in this way.

many cells have the same DNA as they're fertilised from an egg - but there's diffferent genes activated so are diffeernt. e.g. skeletal muscle cells and plant cells.

pg 23 of pack