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introduction

What is DNA? To give a simple answer, it is the molecule of life.  DNA, or deoxyribonucleic acid, determines our physical characteristics - what we look like, our ailments etc. Many also believe that DNA is partly responsible for our behaviour. DNA exists in every single organism, from the smallest virus to the largest mammal. DNA is passed on from generation to generation.

Why is this molecule so fascinating you ask? Well, besides the fact that it is present in like EVERY organism and not to mention the attractive curves on it's double-helical structure, it is the only known molecule that has ability to repli cate istelf.

DNA is like a biological blueprint which contains the instructions for proteins, an essential type of molecule of life.

This website examines the structure of DNA and DNA-related molecules that are involved, the processes of replication, and protein synthesis. Here you will find fun things to do like how to clone a sheep (well, not really), a glossary of te rms for quick and easy reference, and links to sites where you can find gather information to help you in your quest for knowledge.

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cell theory

In order to understand the role of DNA we must first look at the cell theory. It was in 1665 a scientist named Robert Hooke observed the honeycomb-shaped structures of a wedge of cork under his primitive microscope. He described these structures, which were actually cell walls of dead plants, as cells. Hooke's first observations of cells eventually lead to the establishment of the cell theory.

As time passed, microscopes were improved and the biological knowledge base grew. In the 1830's, almost two centuries after Hooke's observations, Robert Brown observed a small and dark-staining sphere inside plant cells. He called this structure a nucleus. Brown's discovery was a key step in the development of the basic cell theory.

In the 1830's, Theodor Schwann and Mathias Schleiden (zoologist and botanist respectively) concluded that the nucleus plays a chief role in the growth and development of living cells. The duo established the basis of the cell theory. The modern cell theory states that all living organisms consist of one or more nucleated cells which are the fundamental unit of function of living organisms and that cells come from existing cells.

chromosomes

The nuclei of cells contain very long threads of nucleic acids and proteins called chromosomes. In the early 1900's, the hypothesis that chromosomes contain hereditary information was gaining acceptance from the biological community. More recent discoveries and investigations has revealed that material within the nucleus indeed contains hereditary information that directs the growth, development, and activities of the cell.

race to reveal the structure of DNA

Once accepted and confirmed that DNA was the source of hereditary information it was a race to discover its structure in hopes of better understanding this fascinating molecule. There were many people who contributed to the discovery of the structure of DNA but it was James Watson and Francis Crick who ultimately developed the first three-dimensional model of a DNA strand. Rosalind Franklin made a significant contribution to the discovery of the structure of DNA with the information she gathered using during X-ray diffraction. At this time, scientists knew that DNA consisted of sugars (deoxyribose sugar), phosphates, and four different nitrogen bases: adenine, guanine cytosine, and thymine. Scientists also discovered, by comparing the DNA in various animals, that the proportion of each nitrogen base in the DNA of different species of animals varies but number of adenine molecules equals to the number of thymine molecules, and the number of guanine molecules equals to the number of cytosine molecules. Using these vital pieces of information, Watson and Crick worked together to evolve the first three-dimensional model of the structure of DNA in 1953. Watson and Crick's model is still in use today.


dna and rna

DNA stands for deoxyribonucleic acid. It's definately the famous nucleic acid - we certainly do hear about it all of the time. However, there are a few other types of nucleic acids that play integral roles in the replication of DNA and the synthesis of proteins. These others are varites of ribonucleic acid, or RNA for short. They are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). 

To understand replication and protein synthesis, the structure of all four of these types of nucleic acids must be understood. In this section, that is exactly what will be examined. There are seperate pages for DNA and RNA, and they can be accessed by using the links directly below.

  1. DNA
  2. RNA

    dna: deoxyribonucleic acid

    DNA stands for deoxyribonucleic acid. Strands of DNA are long polymers built of millions of nucleotides that are linked together. Individually, nucleotides are quite simple, consisting of three distinct parts: 
    1. One of four nitrogen bases 
    2. Deoxyribose (a five-carbon sugar) 
    3. A phosphate group 

    The image below shows a simplified representation of a nucleotide. The P represents the phosphate molecule, the S represents the sugar (deoxyribose), and B represents one of the four nitrogen bases.

    Image: Nucleotide

    The structure of the phosphate group is shown below.

    Image: Phosphate Molecule

    1. Nitrogen Bases

    The four nitrogen bases are:
    • Adenine 
    • Guanine 
    • Cytosine 
    • Thymine 
    Nucleotides are named after which of the four nitrogen bases it has. So the names of the four DNA nucleotides are adenine, guanine, cytosine, and thymine. These will be referred to as A, G, C, and T respectively.  (Note: Throughout this site, the words nucleotide and base are often used to represent the same thing - a nucleotide).

    Adenine and guanine are classified as purines since they are double-ringed molecules. Cytosine and thymine and pyrimidenes due to the fact that they are single-ringed molecules. Structural diagrams of the four bases are shown in the table below. 

    Base Adenine (A) Guanine (G) Thymine (T) Cytosine (C)
    Purine/
    Pyrimidene
    Purine Purine Pyrimidene Pyrimidene
    Chemical 
    Structure *
    Image: Chemical Structure of Adenine Image: Chemical Sturcture of Guanine Image: Chemical Structure of Thymine Image: Chemical Structure of Cytosine
    Simplified 
    Representation
    Image: Simplified Adenine
    Image: Simplified Guanine
    Image: Simplified Thymine
    Image: Simplified Cytosine
    * C = Carbon, N = Nitrogen, O = Oxygen.
    A single line between atoms is a single bond.
    A double line between atoms is a double bond.

    A pyrine binds with a pyrimidene in DNA to form a basepair. Adenine and thymine bind together to form the A-T basepair. Likewise, guanine and cytosine come together to form the G-C basepair. The bases are joined together by weak hydrogen bonds, and it is this hydrogen bonding that produces DNA's familiar double helix shape. An image illustrating the how two bases pair with hydrogen bonding is shown below (The blue lines are the hydrogen bonds.) 

    Image: Hydrogen bonding between bases

    2. Deoxyribose

    Deoxyribose is a five carbon sugar, and to fully understand many of the concepts that are presented later on, one must know the structure of deoxyribose. A visual representation of the sugar and how it relates to the other two components of a nucleotide is shown below in figure 1. 

    Image: Deoxyribose

    The carbons of deoxyribose sugar are numbered sequentially from right to left. The first carbon is 1' (read as one prime), the second is 2' (two prime), and so on. The nitrogenous base attaches to the 1' carbon, and the phosphate group attaches to the 5' carbon. The nucleotide below is covalently bonded to the 3' carbon. This allows for a long strand to be built. An example of a single strand of DNA is shown below. 

    Image: Linked Bases

    Instead of always seeing a huge molecular diagram of a DNA strand, what one often sees in a string of letters, such as "ATCTTAG". This string represents the what bases are in a certain side of a strand of DNA. The above string (ATCTTAG) represents the string "adenine-thymine-cytosine-thymine-thymine-adenine-guanine." 

    DNA has two strands. Whatever nucleotides are in one strand, they rigidly fix the sequence of nucleotides in the other strand due to the way base pairing occurs (A with T, G with C). The two strands are complementary. They aren't identical, but fit together just right. 

    In addition, it must be noted that the two strands are antiparallel. That means that they run in opposite directions. One strand goes in a 5' to 3' direction while the other goes in a 3' to 5' direction. By convention, the strand which goes in the 5' to 3' direction is placed on the left in 2-dimensional drawing. Figure 2 gives a visual example of this concept as well as showing how the strands are complementary. 

    Image: Anti-parallelism

    In this next image, the double-helix shape of DNA is shown. The two strands are clearly visible, one being coloured blue, and the other red. 

    Image: Double Helix

     

     
 

rna: ribonucleic acid

RNA, as previously mentioned, is an acronym for ribonucleic acid. There are many forms of RNA which are quite similar to DNA. All types of RNA are transcribed from DNA in a process called transcription which is examined in detail in the Transcription and Translation section. 

A quick comparison between the two effectively explains RNA generally. 

  1. The 5-Carbon sugar in RNA nucleotides is ribose instead of deoxyribose. (A structural diagram is shown below) 
    Image: Ribose

  2. RNA nucleotides have Adenine, Guanine, and Cytosine as bases, but Thymine is replaced with Uracil (U), which forms a basepair with Adenine. 
  3. DNA is double-helix, but RNA usually is a single strand which can have complex twisted and folded secondary and tertiary structures. 
  4. DNA is typically longer than RNA. 
  5. DNA is generally more stable than RNA. DNA is more resistant to spontaneous and enzymatic breakdown, and damage can be repaired because the opposite strand has complementary information. RNA is more reactive due to a reactive -OH side group on the ribose sugar. Direct repairs are not possible if it is a single strand. 
  6. There are several classes of RNA, each with their own function. 
The types of RNA that we are concerned with are: 
  1. Messenger RNA (mRNA) 
  2. Transfer RNA (tRNA) 
  3. Ribosomal RNA (rRNA) 

1. messenger rna

mRNA is synthesized on DNA and contains the information needed to build a protein. mRNA travels from the nucleus of a cell to ribosomes, the place where protein synthesis occurs, and is read by the ribosomes. The result is a protein. Hence the name, messenger RNA. 

The information that mRNA carries is written in genetic code - a sequence of bases. The code is not complicated - it's like a sentance - a series of words. Each code word is called a codon, a sequence of three adjacent nucleotides that specifies one of twentry amino acids. 

There are 64 possible codons (4 x 4 x 4), and each codon codes for an amino acid. The table below shows which codons code for which amino acids. 


Messenger RNA Codons and Their Corresponding Amino Acids
First Base Second Base Third Base
U C A G
U UUU phenylalanine
UUC phenylalanine
UUA leucine
UUG leucine
UCU serine
UCC serine
UCA serine
UCG serine
UAU tyrosine
UAC tyrosine
UAA stop **
UAG stop **
UGU cysteine
UGC cysteine
UGA stop **
UGG tryptophan
U
C
A
G
C CUU leucine
CUC leucine
CUA leucine
CUG leucine
CCU proline
CCC proline
CCA proline
CCG proline
CAU histidine
CAC histidine
CAA glutamine
CAG glutamine
CGU arginine
CGC arginine
CGA arginine
CGG arginine
U
C
A
G
A AUU isoleucine
AUC isoleucine
AUA isoleucine
AUG methionine *
ACU threonine
ACC threonine
ACA threonine
ACG threonine
AAU asparagine
AAC asparagine
AAA lysine
AAG lysine
AGU serine
AGC serine
AGA arginine
AGG arginine
U
C
A
G
G GUU valine
GUC valine
GUA valine
GUG valine
GCU alanine
GCC alanine
GCA alanine
GCG alanine
GAU aspartate
GAC aspartate
GAA glutamate
GAG glutamate
GGU glycine
GGC glycine
GGA glycine
GGG glycine
U
C
A
G

You might notice that some codons code for the same amino acid. These are known as synonomous codons. For example, GGU, GGC, GGA, and GGG all code for the amino acid glycine. 

The codon AUG is special. It can either specify the amino acid methionine in the middle of a protein, or it can act as an initiation or start signal, which tells the ribosome, "Start translating here." All proteins proteins start out with methionine as their first amino acid, but it is enzymatically removed from some proteins after synthesis. 

Likewise,there are codons which specify the end of a protein. These codons are UAA, UAG, and UGA. 

There is a collinear relationship between DNA, mRNA, and proteins. The beginning of mRNA is DNAs 5' end. The 5' end of mRNA corresponds to the beginning of the amino terminus of the resulting protein. 

the structure of mrna

mRNA in both prokaryotic and eukaryotic cells is divided into three sections: 
  1. The 5' Leader (or just Leader) 
  2. The Coding Region 
  3. The 3' Trailer (or just Trailer) 
The Leader gives physical space to ribosomes so that they can bind to mRNA and move down to the initiation codon. 

The second section, the Coding Region, is the part of mRNA that actually codes for the protein - the codons. 

Finally, there is the Trailer, which is simply a section that comes after the stop codons. 

The diagram below shows the parts of mRNA. 

Image: Simplified Diagram of mRNA

In eukaryotes, mRNA that has just been transcribed from DNA must undergo two post-transcriptional modifications before it can be translated. 

  1. A special methylated version of triphosphate guanine nucleoside is added to the 5' trailer in a process called capping
  2. A Poly-A-Tail, a series of 50 - 150 adenine nucleotides, is added to the 3' end. Their function may be to help transport the mRNA out of the nucleus and determine the number of times mRNA can be translated before it is degraded. 
A simple graphical representation of what happens is shown below. 
Image: mRNA Capping

Eukaryotic mRNA has regions which don't code for proteins. These regions are called Intervening Sequences or introns. Regions which do code for something are called exons. After the primary mRNA transcript is produced, introns must be identified and removed so that only exons remain.

Image: Introns and Exons

Splicing is the process by which introns are removed to produce mature mRNA. It is accomplished in the nucleus of a cell with the aid of splicesomes, large RNA-protein complexes that contain many different enzymes and several kinds of RNA. Splicesomes contain a short piece of RNA that complements base sequences found at either end of just about every intron.

Once a piece of eukaryotic mRNA has been produced, capped, had a poly-a-tail added to it, and once the introns have been removed, it can be translated. Prokaryotic mRNA lacks the methylated cap and the poly-a-tail, and there are no introns so it can be translated right after being transcribed.

One final note, mRNA can be polycistronic. That is, it can contain coding regions for producing more than one polypeptide. Each region contains its own start and stop codons so that seperate proteins are produced.

2. transfer rna

Transfer RNA, or tRNA for short, translates the language of nucleotides into the language of amino acids. It carries amino acids and places them in a protein that is being produced according to the instructions of mRNA.

Each tRNA molecule consists of approximately 90 nucleotides, but when it's longer when it's first produced. To reach its final state, introns are removed, and special enzymes remove segments from each end of it and change some of the bases so that it has more than four types of nucleotides. Finally, three nucleotides are added to the 3' end of every tRNA produced: CCA. In its mature form, the structure of tRNA is quite complex, but to simplify it, imagine a 3-leafed clover. That is the approximate shape since tRNA has 3 loops (the leafs) and one stem.

tRNA has two key features.

  1. First of all, it can be covalently linked to an amino acid. A charging enzyme attaches an amino acid to the -CCA of the tRNA. The enzymes recognize each particular type of tRNA and link it to its appropriate amino acid. a tRNA with its amino acid attached to it is referred to as a charged amino tRNA. There are types of tRNAs for each of the 20 amino acids, but there are actually more due to synonomous codons.
  2. Each tRNA has its own special anticodon which recognizes specific codons. The diagram below shows the concept of codon and anticodon.

Anticodon/codon

3. ribosomal rna

rRNA, or Ribosomal RNA, contributes significantly to the structure of the ribosomes in a cell. mRNA, and tRNA work together the the ribosomes to synthesize proteins.

In eukaryotes, rRNA is transcribed exclusively within the nucleolus while other types of RNA are synthesized throughout the nucleus. After being produced, long primary rRNA strands are processed at once by a special enzyme to yield the specific shorter strands of rRNA that are needed for ribosome assembly.

In eukaryotes, there are three forms of rRNA:

  1. 18 S
  2. 5.8 S
  3. 28 S
There is also a 5 S form, but it is transcribed from a seperate gene and prepared outside of the nucleolus. In case you are wondering, S is a sedimentation or density unit that is used in describing the results of ultracentrifugation and refelcts the size and shape of a molecule or a particle. The larger the value of S is, the bigger the particle is.

rRNA forms the skeleton of ribosomes. The remainder of the ribosomes is comprised of proteins made in the cytoplasm. They enter the nucleus and then the nucleolus and then join rRNA. The assembly of ribosomes is completed in the cytoplasm.

Completed ribosomes have two parts:

  1. 60 S subunit
  2. 40 S subunit
The 60 S subunit contains the 28 S rRNA, the 5.8 S rRNA, the 5 S rRNA, and around 45 to 50 different proteins. The 40 S subunit contains the 18 S rRNA and around 30 different proteins. The final total size of the completed ribosome is around 80 S and half of the mass is proteins.

Ribosomes have specific attachment sites that allow tRNA molecules and mRNA to be in the proper close contact that they require to synthesize proteins. Two of these sites are tRNA pockets called the P site and the A Site. The other sites are mRNA grooves. There is also a site where an enzyme called peptidyl transferase works to form bonds between adjacent amino acids. If you are a bit confused about this last bit, don't worry. It's all covered in Transcription and Translation.


1998 ThinkQuest Team#18617, George Ma, Justin Wong, Liam Stewart

 

dna replication

DNA is unique among all known molecules because it is the only one that is capable of duplicating itself. The process of duplication is called replication.

Replication is somewhat complex, but what basically happens is that the two complementary strands which form the DNA molecule unzip and then are used as templates from which new new strands are made as free nucleotides combine with their complementary bases.

Replication of DNA is semi-conservative. That is, one side of each new DNA strand is "old" and the other side is "new".

Image: A Simple Diagram of Replication

nucleoside triphosphates

Before the steps of replication are looked at, let's just briefly examine nucleoside triphosphates.

Replication involves large numbers of free nucleoside triphosphates. A nucleoside triphosphate is much like a nucleoside except that instead of having one phosphate molecules, it has three. A representation of a nucleoside triphosphate is shown below.

Image: Simplified Diagram of a Nucleoside Triphosphate

In the diagram, P represents a phosphate molecule, S represents a sugar molecule (deoxyribose or ribose), and B represents the base. There are eight types of nucleoside triphosphates involved in replication. They are:

  • dATP - deoxyribose adenosine triphosphate
  • dTTP - deoxyribose thymine triphosphate
  • dCTP - deoxyribose cytosine triphosphate
  • dGTP - deoxyribose guanine triphosphate
  • ATP - ribose adenosine triphosphate
  • TTP - ribose thymine triphosphate
  • CTP - ribose cytosine triphosphate
  • GTP - ribose guanine triphosphate

These molecules will pair with the bases on the template strands during the replication process. The high energy of the triphosphates is used to form bonds between the nucleotides. The two outermost phosphates are liberated, leaving the innermost group still attached. Once the two outermost phosphates have been released, the nucleoside triphosphate has become a nucleotide.

This remaining phosphate forms a link between the two deoxyribose subunits. The free 3'-OH group of the deoxyribose in the first nucleotide then reacts with the first 5' phosphate of the second nucleotide to form a sugar-phosphate-sugar linkage. The 3'-OH group of the second nucleotide is free to, and will, react with the 5' phosphate of the third nucleotide and so on.

unzipping the dna

All references to 3', 5', and other primes refer to the primes on the new parts of the daughter strands.

The process of replication begins in the DNA molecules at thousands of sites called origins of replication. At these sites, which look like little bubbles, the hydrogen bonds between the bases are broken and the paired bases seperate. The helix begins to pull apart or unwind.

The unwinding of the helix is facilitated by an enzyme called helicase, which is part of the replication complex - a group of enzymes and other proteins that take care of the replication process. There are two replication complexes at each origin of replication. As unwinding continues, they move in opposite directions creating two Y-shaped replication forks. Replication proceeds in both directions until the bubbles meet.

The image below shows an orgin of replication. The green arrows indicate the directions that the helix will unravel in. New bases (in blue) are coming in and attaching to their complementary bases on the old strand.

Image: Origin of Replication

As the strands unwind, another enzyme, gyrase prevents an accumulation of twists by making temporary single-strand nicks in the DNA. Where the DNA is nicked, the helix can unwind around the connected strand. The nick will be sealed later by another enzyme called ligase

Replication complexes also contain single-strand binding proteins to help keep the two template strands apart and a familily of enzymes of vital importance to replcation - DNA polymerases.

adding bases

DNA polyermerase III is the primary enzyme responsible for replication. It's main function is to add the 5' phosphate of a new nucleotide to and existing 3'-OH group. A limitation of DNA polymerase III is that it can't begin a new daughter strand by itself - it requires that there already be a 3'-OH end to add the next nucleotide to.

Though there may already be origins of replication on a strand of DNA, replication does not really begin until an enzyme called primase adds a primer of a few RNA nucleotides in a 5' to 3' direction. This primer provides the free 3'-OH needed by DNA polymerase III. The primer is later removed and replaced by DNA.

Another limitation of DNA polymerase III is that it can only add new bases to the 3'-OH end of a growing strand. New DNA strands always grow from the 5' to the 3' end (of the daughter strand). Since the original DNA strand unzips, replication can occur in a 5' to 3' direction on one side and in a 3' to 5' direction on the other side. But DNA polymerase work in a 3' to 5' direction. This problem is ingeniously solved as we will soon see.

As replication moves from an origin along an unowund segment the addition and joingin of bases on one strand can proceed continually in a 5' to 3' direction. This strand is referred to as the leading strand.

The other parent strand is copied discontinuously, creating a lagging strand. As the leading strand is continuously synthesized, unpaired bases accumulate on the laggin strand, joing with their complementary bases but not to each other as DNA polymerase III is needed for that, until a long enough segment has been created to allow first primes then DNA polymerase III to begin working on it in a 5' to 3' direction. The short segments of newly assembled DNA are called Okazaki fragments. As replication proceeds and nucleotides are added to the 3' end of the Okazaki fragments, they come to meet each other. When DNA polyerase III meets the RNA primer from a previous segment, DNA polymerase I comes along and excises the primer, fills the gap with DNA, and leaves. The Okazaki fragments are joined together by ligase.

The image below shows replication. The helix will unwind in the direction of the green arrow. The yellow bases are RNA molecules - the primer. The purple ellipses are DNA polymerases which are linking the new bases together. They move in the direction of the black arrows.

Image: Replication

As the new strands form, DNA polymerase II moves along the strands and proof-reads them for errors, which we also refer to as mutations.


1998 ThinkQuest Team#18617, George Ma, Justin Wong, Liam Stewart

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protein synthesis

DNA codes for amino acids, the building blocks of life. Amino acids that are linked together are called proteins: molecules that have many functions including support, structure, movement, transport, communication, and disease defense. Protein-containing structures include hair, nails, hooves, cartilage, muscle, hormones, antibodies, blood proteins, and enzymes.

Protein synthesis is the process by which proteins are created from the DNA "blueprints". There are two major processes involved:

  1. Transcription: DNA to RNA
  2. Translation: RNA to proteins

Click the links above for more detail.

transcription

Transcription is the first step in protein synthesis. It is synthesis of RNA under direction from DNA. In many ways transcription is quite similar to DNA replication, except, in this case, instead of new DNA nucleotides being added, RNA nucleotides are added to the DNA to form a RNA strand known as the primary transcript. The primary transcript eventually goes on to become a messenger RNA (mRNA) strand after some modification. It is mRNA that directs the following step of protein synthesis, translation.

Transcription begins when RNA polymerase breaks the hydrogen bonds between the two sides of a DNA strand and begins adding RNA nucleotides. RNA polymerase first binds to promoter regions, which include the intiaition site and several other nucleotides, on the DNA strand. However, RNA polymerase can not recognize the promoter regions on its own. Thus, transcription factors search along the DNA strand for promoter regions and the RNA polymerase recognizes the transcription factors.

When RNA polymerase sucessfully binds to a promoter region, it begins adding RNA nucleotides. Since RNA polymerase only works in a 5' to 3' direction only one side of the DNA strand is active in transcription. The addition of RNA nucleotides is directed by the DNA. Specific nucleotide sequences on the DNA strand mark initiation and termination sites, when transcription begins and ends. The initiation sequence, termination sequence, and all the intervening nucleotides together are colectively known as a transcription unit.

As in DNA replication, bases that are complementary to those on the original DNA strand are added in a 5' to 3' direction. However, RNA lacks the base thymine (thymine is specific to DNA),which is complementary to adenine. Instead the RNA has the base uracil. Thus, when adding complementary bases during transciption the complementary base pairings are Cytosine for Guanine, as in DNA replication, and Adenine for Uracil. These nucleotides are added to the DNA strand by RNA polymerase. RNA polymerase unwinds one turn of the DNA helix at a time and adds nucleotides. When one turn of the helix has been completed and the next is about to begin unwinding, the newly added RNA nucleotides seperate from the DNA strand and the DNA strand rewinds. Nucleotide addition progresses at a rate of about 60 nucleotides per second.

Transcription continues until RNA polymerase reaches a termination site on the DNA strand. This site has a sequence of nucleotides, the most common of which being AATAAA in eukaryotic cells, that tell RNA polymerase to stop adding nucleotides. Thus the formation of the primary transcript has been completed.

In eukaryotic cells, the primary transcript undergoes modification before it becomes messenger RNA (mRNA) and is ready to leave to nucleus and go into the cytoplasm. The 5' end of the molecule, where transcription began, is capped off with a modified form of guanine. This cap serves to protect the mRNA molecule from degredation in the cytoplasm. Also, it serves as a signal to ribosomal subunits in the cytoplasm. At the 3' end of the molecule a poly-A-tail is added, which consists of 30-200 adenine nucleotides. It also protects the mRNA molecule from degredation and helps in the export of the mRNA from the nucleus to the cytoplasm. Also, the molecule is shortened in a process known as RNA splicing. The noncoding regions of the molecule, known as introns, are cut out by splicesomes. This leaves only the functional coding regions, exons, in the mRNA molecule.

Thus transcription is completed and a mRNA molecule is formed. Messenger RNA is now able to leave to nucleus and go to the cytoplasm and perform its function in the next step in protein synthesis, translation.

Proceed to translation

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Translation

Translation translates final mRNA to polypeptides (proteins) through a process that has three steps:

  1. Initiation
  2. Elongation
  3. Termination
Translation involes multiple molecules including mRNA, tRNA, the two ribosomal units and various enzymes and proteins.

Initiation
During initiation, everything is set up for translation. The various components comes together. mRNA attaches to the small ribosomal unit, with the initiator codon, which is always AUG (methionine), being on the unit and the charged tRNA that has the mRNA and binds to the ribosomal unit with three proteins. Once this is done, the complex attaches to the large ribosomal unit with the mRNA-tRNA starting point in the P site of the large unit.

Elongation
During elongation, a tRNA that matches the codon in the A site comes in. With the help of the enzyme peptidyl transferase, an amino bond is formed between the two amino acids, the enrgy coming from the bond between the first amino acid and its tRNA. Once the bond is made, the now uncharged tRNA drifts away, and the whole complex moves over three bases (to the right). Each of the three base mRNA sequences, codons, instruct tRNA to bring a specific amino acid to the ribosome. This step repeats until a specific codon called the stop codon is reached. Termination now occurs.

A table of mRNA codons and what function they serve follows.


Messenger RNA Codons and Their Corresponding Amino Acids
First Base Second Base Third Base
U C A G
U UUU phenylalanine
UUC phenylalanine
UUA leucine
UUG leucine
UCU serine
UCC serine
UCA serine
UCG serine
UAU tyrosine
UAC tyrosine
UAA stop **
UAG stop **
UGU cysteine
UGC cysteine
UGA stop **
UGG tryptophan
U
C
A
G
C CUU leucine
CUC leucine
CUA leucine
CUG leucine
CCU proline
CCC proline
CCA proline
CCG proline
CAU histidine
CAC histidine
CAA glutamine
CAG glutamine
CGU arginine
CGC arginine
CGA arginine
CGG arginine
U
C
A
G
A AUU isoleucine
AUC isoleucine
AUA isoleucine
AUG methionine *
ACU threonine
ACC threonine
ACA threonine
ACG threonine
AAU asparagine
AAC asparagine
AAA lysine
AAG lysine
AGU serine
AGC serine
AGA arginine
AGG arginine
U
C
A
G
G GUU valine
GUC valine
GUA valine
GUG valine
GCU alanine
GCC alanine
GCA alanine
GCG alanine
GAU aspartate
GAC aspartate
GAA glutamate
GAG glutamate
GGU glycine
GGC glycine
GGA glycine
GGG glycine
U
C
A
G

Termination
Since there are no tRNAs that bind with the stop codons, useless proteins plug up the A site. The bond between the last tRNA and the last amino acid on the now long poly peptide is broken and the whole complex breaks up.

It should be noted that mRNA can have many ribosome complexes translating it at the same time - polysomes. The ribosomes are spaced at regular intervals and translate the mRNA, allowing for fast production of many proteins.


Glossary of Terms


AB CD EF GH IJ KL MN OP QR ST UV WX YZ

A

amino acid - an organic molecule that has both amino and carboxyl groups; amino acids constitute the monomers (basic units) of proteins.

anticodon - a specific base triplet located on one end of a tRNA molecule that recognises the complementary codon on an mRNA molecule.

A site - the binding site on a ribosome that holds the tRNA carrying the next amino acid to be added to a growing polypeptide chain.


B

base pair substitution - a type of point mutation; the replacement of one complementary set of nucleotides by another pair.


C

codon - a three-nucleotide sequence of DNA or mRNA that codes for a specific amino acid or termination signal; the basic unit of the genetic code.


D

deletion - the mutational loss of a nucleotide from a gene.

deoxyribose - the sugar component of DNA. Deoxyribose has one fewer hydroxyl group than ribose.

DNA ligase - a DNA replication enzyme that catalyzes the formation of covalent bonds between the 3' end of a new DNA fragment and the 5' end of the growing strand.

DNA polymerase - an enzyme that catalyzes the formation of new DNA at a replication fork in the 5' to 3' direction by adding nucleotides to the existing strand.
There are three types of DNA polymerase in prokaryotic cells; polymerase III adds nucleotides to a growing strand in a 5' to 3' direction; polymerase I removes the RNA primer and replaces it with DNA; and polymerase II proof reads DNA for mutations.

double helix - the natural form of DNA, refering to its two complementary neucleotide strands which wind into a spiral shape due to hydrogen bonds.


E

elongation - the stage in translation where amino acids are added one by one to the first amino acid.

exons - the portion of a eukaryotic gene that is expressed; exons are divided from eachother by introns.


F

frameshift mutation - a mutation that occurs when the number of nucleotides inserted or deleted is not a multiple of 3; results in incorrect codon grouping.


H

helicase - an enzyme which promotes the unwinding of the DNA strand.


I

initiation - the frist stage of translation; mRNA, tRNA with the first amino acid, and the two ribosomal units are brought together

insertion - a mutation where one or more nucleotide pairs is/are added to a gene.

introns - the noncoding regions of a gene. See exons.


L

lagging strand - the DNA strand which is discontinuously synthesized in direction away from the replication fork.

leading strand - the new complementary DNA strand which is synthesized continuously in the 5' to 3' direction.


M

missense mutations - the most common type of mutation involving a base-pair substitution within a gene that changes a codon, but the new codon makes sense in that it still codes for an amino acid.

messenger RNA (mRNA) - a type of RNA that is synthesised from DNA in the genetic material. It attaches to ribosomes in the cytoplasm and specifies the structure of a protein.

mutagen - a chemical or other physical agent that interacts with DNA to cause a mutation.

mutations - rare changes in the DNA of genes which eventually lead to genetic diversity.


N

nonsense mutations - a mutation that changes a codon for an amino acid to one of the three stop codons. This usually results in a shorter nonfunctional protein.

nucleolus - a specialized structure within the nucleus formed by various chromosomes. It is active in the synthesis of ribosomes.

nucleoside - an organic molecule made up of a nitrogenous base attached to a five carbon sugar.

nucleotide - the building block of a nucleic acid; it consists of a five carbon sugar covalently bonded to a nitrogenous base and a phosphate group.

nucleus - the organelle of an eukaryotic cell which contains chromosomes.


O

origins of replication - the locations on a DNA strand where the strand begins "unzipping".


P

point mutations - a chromosomal change at some single nucleotide of a gene.

poly-A-tail - a nucleotide complex attached to the 3' end of and mRNA molecule that stops degredation and helps translation.

polysome - a group of several ribosomes attached to the same single mRNA molecule.

primase - a enzyme which adds RNA primer to the beginning of a new strand (one primer on the leading strand and one primer per Okazaki fragment.

primer - a pre-existing DNA strand bound to the template DNA to which nucleotides must be added during DNA synthesis.

promoter - a DNA codon found near the beginning of a gene that tells RNA polymerase where to start transcribing RNA.

P site - the binding site on a ribosomal unit that holds the tRNA carrying a growing polypeptide chain.


R

replication fork - a Y-shaped point (fork) on a replicating DNA strand where new DNA is being formed by the addition of nucleotides.

ribose - the five carbon sugar component of RNA.

ribosome - a cell organelle produced in the nucleolus. It consists of two subunits and is

ribosomal RNA (rRNA) - forms the structure of ribosomes that coordinate the sequential joining of tRNA molecules to the series of mRNA codons.

RNA polymerase - an enzyme that links the growing chain of ribonucleotides during transcription.

RNA splicing - the removal of noncoding portions of the RNA molecule after its initial sysnthesis.


S

splicesome - an assembly that interacts with the ends of RNA introns. It cuts out an intron and joins two adjacent exons.

substitutions -


T

termination - the final stage of protein synthesis. A stop codon in conjunction with a releasing factor signals the ribosome to stop adding amino acids and release the peptide chain.

transcription - the transfer of information from a DNA molecule into an RNA molecule.

transfer RNA (tRNA) - a RNA molecule that interprets mRNA nucleotide codons and picks up the specific amino acids which the mRNA code for.

translation - the conversion of information from a RNA molecule into a polypeptide.

triplet code - a set of three nucleotides that specify the amino acids for polypeptide chains.

THE MEANING OF THE GENE

To a biologist, Gene?has a very specific and not terribly intriguing definition ?a sequence of DNA building blocks that tells a cell how to string together amino acids in a particular order to manufacture a particular protein. A collagen gene specifies the tightly entwined collagen protein that builds connective tissue; a fibrin gene specifies a key component of the blood clotting apparatus. It is the repertoire of proteins produced in different cells, at different times, that guides our development from a fertilized ovum to a many trillion-celled adult, distinguishing nerve from muscle, fat from bone along the journey. A missing or malfunctioning gene can alter a protein in a way that causes disease ?a clotting factor is absent in hemophilia; a cell surface channel for salts obliterated in cystic fibrosis. The effects of many genes add to mold traits, and the expression of nearly all genes is fine tuned by the environment. Because of our experiences, we are much more than the biochemical information stitched into our genes.

Once called by such colorful names as gemmules and stirps, plastidules and idioblasts, a gene is a unit of inheritance, a packet of instructions passed from one cell generation to the next. Whatever its name, the gene has held different meanings for different individuals across the landscape of time:

To seven-year-old Molly Nash, gene means both sickness and health -- an abnormal gene caused the Fanconi anemia that would have killed her, but not for a gift of the normal version of the gene from her newborn brother, Adam, conceived to save her.

To Jesse Gelsinger, an 18-year-old who died in a gene therapy experiment in 1999, gene meant a risk taken ?and tragically realized.

To folksinger Arlo Guthrie, gene means passing age 45 without showing signs of the Huntington Disease that he saw slowly claim his father, legendary folksinger Woody Guthrie.

To one in seven cats in New England, gene means extra toes.

To Adolph Hitler and others who have dehumanized those not like themselves, the concept of gene was abused to justify genocide.

To a smoker, a gene may mean whether or not lung cancer develops.

To a redhead in a family of brunettes, gene means an attractive variant.

To a 39-year-old woman whose mother, aunt and three sisters all suffered from breast or ovarian cancer, the absence of a particular gene means escape from their fate ?and survivor guilt.

To a lucky one percent of the population, gene means a mutation that robs T cells of a surface protein that enables HIV to enter. They cannot become infected with HIV.

To Andre Agassi and Steffi Graf, gene means the expectation that their son, still a fetus, will one day be a tennis champ, like themselves. They could be wrong.

To defense attorneys for Richard Speck, killer of nine student nurses in the 1960s, extra genes on Speck뭩 extra Y chromosome meant he wasn뭪 responsible for his behavior ?an association that has not held up.

To people who object to genetically modified foods, gene means fear and tampering with nature.

To people with diabetes, gene means tampering with nature, and also easier and safer medical treatment, in the form of bacteria that produce human insulin.

To a child suffering from severe vitamin A deficiency, genetically modified yellow rice that produces beta carotene may mean health, even life.

To an elephant that lives on the African savannah and one that lives in the forest, a gene means that they cannot mate with each other -?their species diverged from a shared ancestor 2.6 million years ago.

To a forensic entomologist, a gene means a clue in the guts of maggots devouring a corpse to the identity of a victim or criminal.

To Tommie Lee Andrews, gene meant jail, as the first trial to use DNA fingerprinting established him as a rapist.

To scientists-turned-biotech entrepreneurs, gene means money.

To those who inherit a particular gene variant on chromosome 4, gene means a very long life -- if they can avoid accidents.


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