Protein Synthesis and Cellular Control

Genes are sections of DNA found on chromosomes. Genes code for proteins, including enzymes. Proteins are made from amino acids and different proteins have a different number and order of amino acids. Each amino acids is coded for by a sequence of three bases (called a triplet or codeon) in a gene. 

Example

G-T-C-T-C-A-T-C-A codes for and order of Valine-Serine-Serine as G-T-C is the codeon for Valine and T-C-A is the codon for Serine.

Some amino acids are coded for by more than one triplet, e.g. the amino acid proline can be coded for by four differnet base triplets: CCT, CCC, CCA and CCG. Glutamine can be coded for by two different triplets: CAA and CAG. 

Other triplets are used to tell a cell when to start and stop production of the protein- these are called start and stop codons. They are found at the beginning and end of the gene. 

Example- AUG is a start codon, which also codes for the amino acid methionine. TAG is a stop codon, but doesnt code for an amino acid. 

DNA molecules are found in the nucleus of the cell, but the organelles for proteins synthesis are found in the cytoplasm. DNA is too large to move out of the nucleus, so a section is copied into RNA. This is called transcription. The RNA leaves the nucleus and joins with a ribosome where it can be used to synthesis a protein. This is called translation. 

Messenger RNA (mRNA)

mRNA is a single polynucleotide strand. It is made in the nucleus during transcription. mRNA carries the genetic code from the DNA in the nucleus to the cytoplasm, where it is used to mae a protein during translation. In mRNA, groups of three adjacent bases are usually called codons. 

Transfer RNA (tRNA)

tRNA is a single polypeptide strand that is folded into a clover shape. Hydrogen bonds between specific base pairs hold the molecule in this shape. Every tRNA molecule has a specific sequence of three bbases at one end called an anticodon. They also have an amino acid binding site at the other end. tRNA is found in the cytoplasm where it is involved in translation. It carries the amino acids that are used to made proteins to the ribosomes. 

1) RNA polymerase attaches to the DNA- Transcription starts when RNA polymerase attaches to the DNA double helix at the beginning of a gene. Hydrogen bonds between the two DNA strands in the gene break, separating the strands, and the DNA molecule uncoils. One of the strands is the used as a template to make and mRNA copy. 

2) Complementarty mRNA is formed- The RNA polymerase lines up free RNA nucleotides alongside the template strand. Complementary base pairing means that the mRNA strand ends up being a template strand (except the base T is replaced by U). Once the RNA nucleotides have paired up with their specific bases om the DNA strand they are joined together, forming and mRNA molecule.

3) RNA polymerase moves down the DNA strand- The RNA polymerase moves along the DNA, separating the strands and assembling the mRNA strand. The hydrogen bonds between the uncoiled strands of DNA re-form once the RNA polymerase has passed by and the strand coils back into a double helix.

4) mRNA leaves the nucleus- When RNA polymerase reaches a stop codon, it stops making mRNA and detaches from the DNA. the mRNA moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm.  

Translation takes place at the ribosomes in the cytoplasm. During translation, amino acids are joined together by a ribosome to make a polypeptide chain (protein), following the sequence of codons carried by the mRNA.

1) The mRNA attaches itself to a ribosome and tRNA molecules carry amino acids to the ribsome. 

2) A tRNA molecule, with an anticodon that is complementary to the first codon on the mRNA, attaches itself to the mRNA by complementary base pairing. A second tRNA molecule attaches itself to the next codon on the mRNA in the same way. 

3) The two amino acids attached to the tRNA molecule are joined by a peptide bond. The first tRNA molecule moves away, leaving its amino acid behind.

4) A third tRNA molecule binds to the next codon on the mRNA. Its amino acid binds to the first two and the second tRNA molecule moves away. This process continues, producing a chain of linked amino acids, until there is a stop codon on the mRNA molecule. 

5) The polypeptide chain then moves away from the ribosome and translation is complete.

Genetic control of protein production in prokaryotes often involves operons. An operon is a section of DNA that contains structural genes, control elements and sometimes a regulatory gene. The structural genes code for useful proteins, such as enzymes- they are all transcribed together. The control elements include a promoter (a DNA sequence located before the structural genes that RNA polymerase binds to) and an operator (a DNA sequence that proteins called transcriptio factors bind to). The regulatory gene codes for a transcription factor. 

Transcription factors
   A transcription factor is a protein that binds to DNA and switches genes on or off by starting or stopping transcription. Factors that start transcription are called activators and those that stop transcription are called repressors. The shape of a transcription factor determines whetjer it can bind to DNA or not, and cna be altered by the binding of some molecules. this means that the amount of some some molecules in an environment or a cell can control the synthsis of some proteins by affecting transcription factor binding.

Example- when Lactose is not present the regulatory gene produces the lac repressor, which bins to the operator site and block transcription. When lactose is present, it binds to the repressor, changing the shpe so that it can no longer bind to the operator site. RNA polymerase can now begin transcription of the structural gene.  

Some proteins produced by protein synthesis aren't active- they have to be activated to work. Protein activation is controlled by molecules such as horomones and sugars. 

cAMP

Some moleucles that control protein activation work by binding to cell membranes and triggering the production of cyclic AMP inside the cell. cAMP then activates proteins inside the cell by altering their 3D structure.

Example

PKA is an enzyme made of four subunits. When cAMP isn't bound, the four units are bound together and are inactive. When cAMP binds, it causes a change in the enzyme's 3D structure, releasing the active subunits-PKA is now active. 

A body plan is the general structure of an organism, e.g. the Drosophila fruit fly has various body parts that are arranged in a particular way. 

Proteins control the development of a body plan- they help set up the basic body plan so that everything is in the right place. The proteins that control body plan development are coded for by genes called homeotic genes. Similar homeotic genes are found in animals, plants and fungi, which means that body plan development is controlled in a similar wat in flies, mice, humans. 

How do homeotic genes contol development?
   Homeotic genes have regions called homeobox sequences that code for a part of the protein called the homeodomain. The homeodomain binds to specific sites on DNA, enabling the protein to work as a transcription factor. The proteins bind to DNA at the start of developmental genes, activating or repressing transcription and so altering th production of proteins involved in the development of the body plan 

Some cells die and break down as a normal part of development. this is a highly controlled process called apoptosis. Once apoptosis has been triggered the cell is broken down in a series of steps:

•  Enzymes are released from lysosomes inside the cell. The enzymes break down cell components, e.g. proteins and DNA. 
• The cell shrinks and begins tofragment.
• Phagcytes engulf and digest the cell fragments.

Apoptosis is involved in the development of body plans- mitosis and differentiation create the bulk of the body plarts and the apoptosis refines the parts by removing the unwanted structures. 

Example

•    When hands and feet first develop the fingers and toes are connected. They are only separated when cells in the connecting tissue undergo apoptosis. 
• An excess of nerve cells are produced during the development of the nervous system.   

What are mutations?

Any change to the base sequence of DNA is called a mutation. The types of mutations that cn occur include:

• Substitution- One base is swapped for another base, e.g. ATGCCT becomes ATTCCT (G is swapped for T).
• Deletion- one or more bases are removed, e.g. ATGCCT becomes ATCCT (G is removed). 
• Insertion- one or more bases are added, e.g. ATGCCT becomes ATGACCT (A is added).
• Duplication- one or more bases are repeated, e.g. ATGCCT becomes ATGCCCCT (CC is repeated).
• Inversion- a sequence of bases is reversed, e.g. ATGCCT cecomes ATCCGT (GCC is reversed to CCG). 

Some mutations have a huge effect on the base sequence of a gene. For example, adding or deleting a base changes the number of bases present causing a shift in all the base triplets that follow. This is when an insertion or deletion changes the way a base sequence is read. The the earlier a frameshift mutation appears in the base sequence, the more amino acids are affected and the greater the mutation effect on the protein. 

Original gene- T-A-T-A-G-T-C-T-T 

Original protein- Tyrosine-Serine-Leucine

Mutated gene- T-A-T-(A)-G-T-C-T-T 

Mutated protein- Tyrosine-Valine 

Different mutations affect proteins in different ways. Some mutations can have a neutral effect on a protein's function. They may have a neutral effect because:

• The mutation changes a base in a triplet, but the amino acid that the triplet codes for doesn't change. This happenes because some amino acids are coded for by more than one triplet. Example- Both TAT and TAC code for tyrosine, so if TAT is changed to TAC the amino acid won't change.
• The mutation produces a triplet that codes for a different amino acid, but the amino acid is chemically similar to the original so it function like the original amino acid. Example- Arginine and lysine are coded for by similar triplets. A substitution mutation can swap the amino acids but this would have a neutral effect on a protein as the amino acids are chemically similar.
• The mutated triplet codes for an amino acid not involved with the protein's function. example- if the affected amino acid is located far away from an enzyme's active site, the protein will work as it normally does. 

Some mutations do affect a protein's function- thay can make a protein more or less active, e.g. by changing the shape of an enzyme's active site. If protein function is affected it can have a beneficial or harmful effect on the whole organism. 

Mutations with beneficial efffects
   These have an advantageous effect on an organism,i.e. they increase its chance of survival.

Example- Some bacterial enzymes brak down certain antibiotics. Mutations in the genes that code for these enzymes could make them work on a wider range of antibiotics. This is beneficial to the bacteria becuase antibiotic resistnace can help them to survive. Mutations that are beneficial to the organism are passed on to future generations by natural selection. 

Mutations that have harmful effects
   These have a disadvantageous effect on an organism, i.e. they decrease its chance of survival

Example- Cystic fibrosis (CF) can be casued by a deletion of these bases in the gene that codes for the CFTR protein. The mutated CFTF protein folds incorrectly, so it's broken down. this leads to excess mucus production, which affects the lungs of CF sufferers.