Proteins are chains of amino acids called a polypeptide chain. The chain is pulled into a variety of complex 3-D shapes.

Proteins have four major functions:

1) structural proteins

2) enzymes

3) regulatory proteins

4) transport proteins

- Structural proteins include microtubules, contracting filaments in muscle cells and viral coats.

- Enzymes are proteins that carry out chemical reactions. The enzyme binds with another molecule called a substrate. Some may bind more than one substrate molecule at a time.

The enzyme has an active site were the substrate binds and the reaction occurs. This pocket is produced by unfolding of the polypeptide chain. See Fig 7.2.

- A regulatory protein controls the expression of a gene or the activity of another protein.

- Transfer proteins carry other molecules across membranes or around the body.

These are extra chemical groups attached to proteins to make them function.

Many proteins use single metal ions as cofactors and others use more complex molecules.

In hemoglobin there is a ring-shaped cofactor called heme with a central iron atom. Oxygen binds to the iron atom at the center of the heme. Thus, this co-factor is required in order to tranpsort oxygen throughout your body.

Amino acids: there are twenty amino acids used in making our proteins.

An amino acid contains a central -CH (1) an amino group (NH₂), (2) a carboxyl (-COOH) group and (3) the variable group labeled R. See Fig 7.6.

The amino acids are joined by covalent bonds between carboxyl groups and amino groups to make the peptide chain, with a loss of water.

Primary structure: this is the linear string of amino acids bound with covalent bonds.

Secondary structure: this is done using hydrogen bonds. This can produce an alpha-helix which has some similarities to the double helix of DNA. See Fig 7.9. An alternative structure is a beta- sheet shown in Fig 7.10. This also depends hydrogen bonding.

Tertiary structure: the 3-D folding to a large extent depends on hydrophilic and hydrophobic portions of the side chains. The hydrophilic or water-loving portions stay on the surface of the protein structure. Hydrophobic portions stay at the interior. This results in a roughly globular protein shape. See Figs. 7.11-7.13.

Quaternary protein structure: A combination of more than one polymer chain in the final structure.

Alphabetically, they range from alanine to valine. See table, page 70. You do not need to know the amino acids.

HOW OUR PROTEINS MADE?

Proteins are made using the genetic information on chromosomes. The genetic information is transmitted in two stages:

(1) Transcription: DNA is transcribed into mRNA.

(2) Translation: the mRNA nucleic acid message is translated into an amino acid polypeptide chain. Three nucleotide bases code for an amino acid.

It is usually true that each gene in the DNA gives rise to a single protein. "DNA makes RNA makes protein" is the central dogma of molecular biology (Fig 7.14).

There are 20 amino acids. There are four different bases in mRNA. The bases of mRNA are read in groups of three. These groups of three are called codons. They code for an amino acid. There are four different bases, so 4³ = 64 possible groups of three bases. See Fig 7.15.

mRNA, rRNA and tRNA.

A ribosome is made up of RNA and proteins. The ribosome has two subunits, a 30 S subunit and the 50S subunit. The S values indicates sedimentation rate in an ultracentrifuge.

The RNA in ribosomes is called ribosomal RNA or rRNA.

The codon and anti-codon can recognize each other by base pairing and are held together by hydrogen bonds (Fig 7.18).

There are 20 different amino acids. There are 64 potential codons for the amino acids as shown in Table 7.15. The number of different tRNA molecules is somewhere between 20 in 64.

Some tRNA can read more than one codon because there is its an exception to the complementary based pairing rule, called wobble rules. This only occurs in the three-base-pair sequences of tRNA anti-codon to the mRNA codon. The first base of tRNA can wobble a bit: does not always have to have an exact fit to a complementary base. G-C and U-A are normal. G-U and U-U use wobble rules. See Fig 7.19.

Each tRNA has its own enzyme, amino acid tRNA synthetase which attaches the amino acid to the tRNA. The Fig 7.20.

tRNA has four branches and three of these have loops. The amino acid is on the end of the unlooped branch. See Fig 7.21. One loop called the anti-codon loop has three bases, the anti-codon for the amino acid at the other end of the tRNA.

The bases of mRNA are read in groups of three, starting at the five prime (5') end. The reading begins with the start codon, AUG. There may be several AUG's in the mRNA chain so there are several possible reading frames to make protein.

Fig 7. 24 shows the components being initially assembled to start proteins synthesis. The mRNA must have a start codon (AUG) and an S-D sequence for this to get rolling.

(1) mRNA with the start codon and S-D sequence.

(2) a small rRNA subunit with the start anti-codon.

(3) f-met tRNA.

These all assemble. The large rRNA subunit comes in and binds to the small subunit.

- The second tRNA comes in and binds to the "A" site.

- The fMet amino acid is transferred from the "P" site to amino acid No. 2 at the "A" site.

- The ribosome moves down the mRNA one codon sequence. The empty tRNA which had carried in the fMet gets bumped off.

- The tRNA with the growing polypeptide chain is now on the "P" site.

- A third tRNA comes in with its own amino acid comes into the "A" site.

- The growing polypeptide chain is moved to the amino acid on the "A" site.

- The ribosome then moves another three base sequence along the mRNA bumping off the empty tRNA from the "P" site. And the process is repeated. See Fig 7.25.

This is an energy intensive process. The arrival and sideways shuffling is supervised by proteins called the elongation factors. The elongation factors require energy to move tRNA and ribosomes.

The end of the message to make protein on mRNA's is marked by a stop codon. These are UGA, UAG, and UAA. There are no tRNAs to read these. So tRNA just stops. Proteins known as release factors read the stop signal and chop off the completed peptide chain. The ribosome then disassembles. See Fig 7.26.

In a strand of bacterial mRNA there may be several "open reading frames," each with its

own start codon and S-D sequence to make several protein molecules. This is not found in higher organisms. See Fig 7.27.

Several ribosomes can move along the same mRNA about a hundred bases apart, making multiple copies of the protein. This can happen in people and bacteria. See Fig. 7.28.

In bacteria a ribosome can start translating the mRNA message into protein before the DNA has finished making the mRNA. See Fig 7.29. This cannot happen in us because our DNA is making RNA in the nucleus and the RNA makes protein outside the nucleus.

If the mRNA is defective and there is no stop codon, the ribosomes will sit there stalled. See Fig 7.30. Bacteria have a special tmRNA that brings in a stop codon. Protein synthesis can now conclude. See Fig 7.31.

The protein just made is defective. The tmRNA does not have the right codon to make a correct protein. The tmRNA added a codon for a tail-sequence of amino acids that allows this defective protein to be destroyed. The bad protein is gobbled up by tail-specific protease. See Fig 7.32.

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