The Protein Synthesis Process

Now let's look at the order of events in the synthesis of our protein from our sample mRNA :

• A ribosome binds to mRNA with the AUG codon in the P-site and the UUU codon in the A-site.
• An amino acyl-tRNA (anti-codon = UAC) with an attached methionine comes in to the P-site of the ribosome
• An amino acyl-tRNA (anti-codon = AAA) with an attached phenylalanine comes in to the A-site of the ribosome
• A chemical bond forms between the methionine and phenylalanine (in a protein, this covalent bond is called a peptide bond).
• The methionine-specific tRNA leaves the P-site and goes off to collect another methionine
• The ribosome shifts so that the P-site now contains the UUU codon with the attached phenyl-alanine tRNA and the next codon (ACA) now occupies the A-site.
• An amino acyl-tRNA (anti-codon) with an attached threonine comes in to the A-site of the ribosome.
• A peptide bond forms between the phenylalanine and the threonine.
• The phenylalanine-specific tRNA leaves the P-site and goes off to find another phenylalanine.
• The ribosome shifts down codon so that the cease sequence is now in the A-site. On encountering the cease sequence:
• The ribosome detaches from the mRNA and splits in to its parts
• The threonine-specific tRNA releases its threonine and leaves
• The new protein floats away
• Several ribosomes can attach to a molecule of mRNA after another and start making proteins. So several proteins can be made from mRNA. In fact, in E. coli bacteria, translation of the mRNA begins even before transcription is completed.

Building a Protein: Transcription

Building proteins is much like building a house:

1. The master blueprint is DNA, which contains all of the information to build the new protein (house).
2. The working copy of the master blueprint is called messenger RNA (mRNA), whic­h is copied from DNA.
3. The construction site is either the cytoplasm in a prokaryote or the endoplasmic reticulum (ER) in a eukaryote.
4. The building materials are amino acids.
5. The construction workers are ribosomes & transfer RNA molecules.

Let's look at each phase of the new construction more closely.
       In a eukaryote, DNA never leaves the nucleus, so its information must be copied. This copying method is called transcription & the copy is mRNA. Transcription takes place in the cytoplasm (prokaryote) or in the nucleus (eukaryote). The transcription is performed by an enzyme called RNA polymerase. To make mRNA, 


RNA polymerase :

               Binds to the DNA strand at a specific sequence of the gene called a promoter Unwinds & unlinks the strands of DNA. Makes use of the DNA strands as a guide or template

               Matches new nucleotides with their complements on the DNA strand (G with C, A with U -- keep in mind that RNA has uracil (U) in lieu of thymine (T)). Binds these new RNA nucleotides together to form a complementary copy of the DNA strand (mRNA). Stops when it encounters a termination sequence of bases (cease codon) mRNA is happy to live in a single-stranded state (as against DNA's desire to form complementary double-stranded helixes). In prokaryotes, all of the nucleotides in the mRNA are part of codons for the new protein. However, in eukaryotes only, there's additional sequences in the DNA & mRNA that don't code for proteins called introns.

This mRNA is then further processed : 

               Introns get cut out

               The coding sequences get spliced together

               A special nucleotide "cap" gets added to finish

               A long tail consisting of 100 to 200 adenine nucleotides is added to the other finish

               No knows why this processing occurs in eukaryotes. Finally, at any moment, plenty of genes are being transcribed simultaneously according to the cell's needs for specific proteins.

The working copy of the blueprint (mRNA) must now go the construction site where the workers will build the new protein. If the cell is a prokaryote such as an E. coli bacterium, then the site is the cytoplasm. If the cell is a eukaryote, such as a human cell, then the mRNA leaves the nucleus through giant holes in the nuclear membrane (nuclear pores) & goes to the endoplasmic reticulum (ER).

How does DNA encode the information for a protein?

How does DNA encode the information for a protein? 

      ~~> There's only DNA bases, but there's twenty amino acids that can be used for proteins. So, groups of nucleotides form a word (codon) that specifies which of the twenty amino acids goes in to the protein (a 3-base codon yields 64 feasible patterns (4*4*4), which is over to specify twenty amino acids. Because there's 64 feasible codons & only twenty amino acids, there is some repetition in the genetic code. Also, the order of codons in the gene specifies the order of amino acids in the protein. It may need anywhere from 100 to one,000 codons (300 to four,000 nucleotides) to specify a given protein. Each gene also has codons to designate the beginning (start codon) & finish (cease codon) of the gene.

What DNA Does

           DNA carry all of the information for your physical characteristics, which are fundamentally determined by proteins. So, DNA contains the instructions for making a protein. In DNA, each protein is encoded by a gene (a specific sequence of DNA nucleotides that specify how a single protein is to be made). Specifically, the order of nucleotides within a gene specifies the order and types of amino acids that must be put together to make a protein.  A protein is made of a long chain of chemicals called amino acids.
Proteins have lots of functions :
        Enzymes that over out chemical reactions (such as digestive enzymes)
        Structural proteins that are building materials (such as collagen and nail keratin)
        Transport proteins that over substances (such as oxygen-carrying hemoglobin in blood)
        Contraction proteins that cause muscles to compress (such as actin and myosin)
        Storage proteins that hold on to substances (such as albumin in egg whites and iron-storing ferritin in your spleen)
Hormones - chemical messengers between cells (including insulin, estrogen, testosterone, cortisol, et cetera)
Protective proteins - antibodies of the immune process, clotting proteins in blood
Toxins - poisonous substances, (such as bee venom and snake venom)

The particular sequence of amino acids in the chain is what makes protein different from another. This sequence is encoded in the DNA where gene encodes for protein.

DNA Replication

• DNA carries the information for making all of the cell's proteins. These proÃ�­teins implement all of the functions of a living organism & decide the organism'Ã�­s characteristics. When the cell reproduces, it's pass all of this information on to the daughter cells.

• Before a cell can reproduce, it must first replicate, or make a replica of, its DNA. Where DNA replication occurs depends on whether the cells is a prokaryote or a eukaryote (see the RNA sidebar on the earlier page for more about the categories of cells). DNA replication occurs in the cytoplasm of prokaryotes & in the nucleus of eukaryotes. Irrespective of where DNA replication occurs, the basic method is the same.

• The structure of DNA lends itself basically to DNA replication. Each side of the double helix runs in opposite (anti-parallel) directions. The beauty of this structure is that it can unzip down the middle & each side can serve as a pattern or template for the other side (called semi-conservative replication). However, DNA does not unzip entirely. It unzips in a small area called a replication fork, which then moves down the whole length of the molecule.

Let's look at the details:

1. An enzyme called DNA gyrase makes a nick in the double helix & each side separates
2. An enzyme called helicase unwinds the double-stranded DNA
3. Several small proteins called single strand binding proteins (SSB) temporarily bind to each side & keep them separated
4. An enzyme complex called DNA polymerase "walks" down the DNA strands & adds new nucleotides to each strand. The nucleotides pair with the complementary nucleotides on the existing stand (A with T, G with C).
5. A subunit of the DNA polymerase proofreads the new DNA
6. An enzyme called DNA ligase seals up the fragments in to long continuous strand
7. The new copies automatically wind up again

Different types of cells replicated their DNA at different rates. Some cells constantly divide, like those in your hair & fingernails & bone marrow cells. Other cells go through several rounds of cell division & cease (including specialized cells, like those in your brain, muscle & heart). Finally, some cells cease dividing, but can be induced to divide to repair injury (such as skin cells & liver cells). In cells that do not constantly divide, the cues for DNA replication/cell division come in the kind of chemicals. These chemicals can come from other parts of the body (hormones) or from the environment.

Fitting Inside a Cell

         DNA is a long molecule. For example, a typical bacterium, like E. coli, has DNA molecule with about six,000 genes (A gene is a specific sequence of DNA nucleotides that codes for a protein. We'll speak about this later). If drawn out, this DNA molecule would be about one millimeter long. However, a typical E. coli is only six microns long (six one-thousandths of a millimeter).So to fit inside the cell, the DNA is highly coiled and crooked in to circular chromosome.

        Complex organisms, like plants and animals, have 50,000 to 100,000 genes on lots of different chromosomes (humans have 46 chromosomes). In the cells of these organisms, the DNA is crooked around bead-like proteins called  histones. The histones are also coiled tightly to form chromosomes, which can be present in the nucleus of the cell. When a cell reproduces, the chromosomes (DNA) get copied and distributed to each offspring, or daughter, cell. Non-sex cells have copies of each chromosome that get copied and each daughter cell receives copies (mitosis). In the coursework of meiosis, precursor cells have copies of each chromosome that gets copied and distributed equally to sex cells. The sex cells (sperm and egg) have copy of each chromosome. When sperm and egg unite in fertilization, the offspring have copies of each chromosome (see How Sex Works).

DNA structure

        DNA is of the nucleic acids, information-containing molecules in the cell (ribonucleic acid, or RNA, is the other nucleic acid). DNA is present in the nucleus of every human cell. (See the sidebar at the bottom of the page for more about RNA & different types of cells). 

The information in DNA :        Guides the cell (along with RNA) in making new proteins that choose all of our biological traits
gets passed (copied) from generation to the next
The key to all of these functions is present in the molecular structure of DNA, as described by Watson & Crick.
        Although it may look complicated, the DNA in a cell is  a pattern made up of different parts called nucleotides. Imagine a set of blocks that has only shapes, or an alphabet that has only letters. DNA is a long string of these blocks or letters. Each nucleotide consists of a sugar (deoxyribose) bound on side to a phosphate group & bound on the other side to a nitrogenous base.

             There's classes of nitrogen bases called purines (double-ringed structures) & pyrimidines (single-ringed structures). The bases in DNA's alphabet are :
                                                                                      adenine (A) - a purine
                                                                                      cytosine(C) - a pyrimidine
                                                                                      guanine (G) - a purine
                                                                                      thymine (T) - a pyrimidine

             Watson & Crick discovered that DNA had sides, or strands, & that these strands were crooked together like a crooked ladder -- the double helix. The sides of the ladder comprise the sugar-phosphate portions of adjoining nucleotides bonded together. The phosphate of nucleotide is covalently bound (a bond in which or more pairs of electrons are shared by atoms) to the sugar of the next nucleotide. The hydrogen bonds between phosphates cause the DNA strand to twist. The nitrogenous bases point inward on the ladder & form pairs with bases on the other side, like rungs. Each base pair is formed from complementary nucleotides (purine with pyrimidine) bound together by hydrogen bonds. The base pairs in DNA are adenine with thymine & cytosine with guanine.