Cellular Metabolism

Chapter 4

Protein Synthesis

How DNA works

DNA codes for proteins, many of which are enzymes.

• Proteins (enzymes) can be used to make all the other molecules a cell needs: carbohydrates, lipids and nucleic acids.

• A segment of DNA that carries the instructions to make (codes for) a protein is called a gene.

Structure of DNA

• DNA and RNA are made up of nucleotides (Polymers) (Monomers)

• A nucleotide has a sugar, a phosphate group, and a nitrogen containing base.

These nucleotides are linked together to form chains or strands.

In DNA two strands are joined by hydrogen bonds.

RNA is single stranded.

Information is stored in DNA in three base units, called codons.

• We can make 64 different codons, but we only use 20 amino acids.

• One codon means “start here”

• Three codons are “stop” codons.

• More than one codon can be used for a particular amino acid.

• Because DNA is in the nucleus, and our “work benches” – ribosomes- are in the cytoplasm, we need a way to get just the information we need to the ribosome.

• We make a copy of the gene we need in messenger RNA. This process is called TRANSCRIPTION. (We have not changed the “language”, just the form of the information.

• An enzyme called RNA polymerase looks at the DNA to find a special region called a promoter. This tells the enzyme where to start copying the DNA.

• It copies the DNA until it comes to a stop codon.

• Because we are eukaryotes, we modify the pre-messenger RNA we have made.

• We cut out the intervening sequences (Introns) and splice the expressed sequences (Exons) back together. This way, we can make more than one protein from a gene!

• Now it is mature mRNA

• The mRNA leaves the nucleus through the pores in the nuclear envelope, and finds a ribosome in the cytosol or on rough E.R.

Ribosome

There are two subunits that make up a ribosome.

The large subunit catalyzes the formation of the peptide bonds between the amino acids.

The small subunit acts as a reader of the RNA.The RNA must be read correctly, or the wrong amino acid will be used. The 3 base sequence the RNA looks at is called the “Reading frame.”

Changing from the “language” of nucleic acids to the “language” of proteins is called TRANSLATION.

Translation• We need a means of getting the correct

amino acid in the correct sequence. For this we use one more type of RNA : transfer RNA (tRNA).

• tRNA is a single strand of RNA that is folded into the shape of a clover. It has an anticodon that matches the codon on the mRNA, and a spot for holding the amino acid that matches the codon.

• To be sure that the correct tRNA always carries the correct amino acid, the two are put together by enzymes that match the anticodon and the amino acid.

• When the mRNA binds to the small subunit of the ribosome it is called initiation. The ribosome looks for the “start” codon, which is always AUG.

Elongation

• The same three steps are repeated until the “stop” codon is read.

1. An amino acid is placed in position on the “A” site of the ribosome

2. The peptide bond is formed.

3. The peptide moves over to the “P” site so that the “A” site is available for the next amino acid. (The old tRNA is released.)

• When a ribosome has moved far enough down the mRNA, a second ribosome can pick up the mRNA and also start reading and translating it. It may be passed on to a third ribosome, and so on. When we have several ribosomes all translating the same mRNA at the same time, it is called a polysome.

Termination

• When the ribosome reads one of the stop codons, there is no matching tRNA. Instead, a protein called a release factor binds to the stop codon, the polypeptide is cut from the last tRNA, and the polypeptide (protein) is released into the ctyoplasm, where other proteins will help fold it.

To Review:• To help you review transcription and translation,

go to http://www.doegenomes.org  Scroll down to the site directory and click on education. Under quick links click on Videos, Webcasts, Graphics and Animations. You should see three topics:

• Transcription/Translation Overview • Transcription Detail • Translation Detail (protein synthesis) • I would suggest you look at all three.

There is a lot of other interesting stuff here too, FYI

Regulation of protein synthesis

• To form each peptide bond requires 3 molecules of ATP. Since each protein can have from 50 to thousands of amino acids, much of the cell’s energy goes into protein synthesis.

• Protein synthesis is regulated at every step of the process. The most energy efficient, is to control protein synthesis by controlling transcription.

Mutations

• A mutation is a permanent, inheritable change in the DNA.

• To be passed on to the next generation, this mutation must be present in the gametes (eggs or sperm).

Why don’t we see more mutations?

• Silent mutations can occur in non-coding (“junk” ) DNA.

• If we change the last codon, in many cases we get the same amino acid.

• We have pairs of chromosomes, so a good gene may “cover” for a bad one.

• We have about 50 enzymes that “police” our DNA looking for changes and fixing them.

Mutations• Mutations can be as small as a change in

one base – a point mutation

• Mutations can be small sections of DNA, entire genes or large pieces of chromosomes that are moved from one place to another by transposons.

• Entire chromosomes may be duplicated (Down syndrome – 3 copies of chromosome 21) or lost.

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Causes of mutations

• Occur naturally

• Due to mutagens:– Radiation– Toxic chemicals – Viruses