RNA Structure and Function

STRUCTURE AND FUNCTION OF RNA

RNA is structurally similar to DNA!

Both nucleic acids are sugar-phosphate polymers and both have nitrogen bases attached to the sugars of the backbone- but there are several important differences.

They differ in composition:

1 The sugar in RNA is ribose, not the deoxyribose in DNA (as we previously learned).
2 The base uracil is present in RNA instead of thymine.


They also differ in size and structure:

1 RNA molecules are smaller (shorter) than DNA molecules,
2 RNA is single-stranded, not double-stranded like DNA.

Another difference between RNA and DNA is in function. DNA has only one function-STORING GENETIC INFORMATION in its sequence of nucleotide bases. But there are three main kinds of ribonucleic acid, each of which has a specific job to do.

		Ribosomal RNAs-exist outside the nucleus in the cytoplasm of a cell in structures called ribosomes. Ribosomes are small, granular structures where protein synthesis takes place. Each ribosome is a complex consisting of about 60% ribosomal RNA (rRNA) and 40% protein.
		Messenger RNAs-are the nucleic acids that "record" information from DNA in the cell nucleus and carry it to the ribosomes and are known as messenger RNAs (mRNA).
		Transfer RNAs-The function of transfer RNAs (tRNA) is to deliver amino acids one by one to protein chains growing at ribosomes.

DNA Replication

REPLICATION OF DNA How is cellular DNA copied?

DNA replication begins with a partial unwinding of the double helix at an area known as the replication fork. This unwinding is accomplished by an enzyme known as DNA helicase. This unwound section appears under electron microscopes as a "bubble" and is thus known as a replication bubble.

As the two DNA strands separate

the enzyme DNA polymerase moves into position at the point where synthesis will begin.

But where does the DNA polymerase enzyme know where to begin synthesis? Is there some sort of marker, a start point?

YES; the start point for DNA polymerase is a short segment of RNA known as an RNA primer. The very term "primer" is indicative of its role which is to "prime" or start DNA synthesis at certain points. The primer is "laid down" complementary to the DNA template by an enzyme known as RNA polymerase or Primase.

The DNA polymerase (once it has reached its starting point as indicated by the primer) then adds nucleotides one by one in an exactly complementary manner, A to T and G to C.

How does the polymerase "know" which base to add?

DNA polymerase is described as being "template dependent" in that it will "read" the sequence of bases on the template strand and then "synthesize" the complementary strand. The template strand is ALWAYS read in the 3' to 5' direction (that is, starting from the 3' end of the template and reading the nucleotides in order toward the 5' end of the template). The new DNA strand (since it is complementary) MUST BE SYNTHESIZED in the 5' to 3' direction (remember that both strands of a DNA molecule are described as being antiparallel. DNA polymerase catalyzes the formation of the hydrogen bonds between each arriving nucleotide and the nucleotides on the template strand.

In addition to catalyzing the formation of Hydrogen bonds between complementary bases on the template and newly synthesized strands, DNA polymerase also catalyzes the reaction between the 5' phosphate on an incoming nucleotide and the free 3' OH on the growing polynucleotide (what we know is called a phosphodiester bond!). As a result, the new DNA strands can grow only in the 5' to 3' direction, and strand growth must begin at the 3' end of the template, right? Again, note that a phosphodiester bond is formed between the 3' OH group of the sugar and the 5' phosphate group of the incoming nucleotide.

Because the original DNA strands are complementary and run antiparallel, only one new strand can begin at the 3' end of the template DNA and grow continuously as the point of replication (the replication fork) moves along the template DNA. The other strand must grow in the opposite direction because it is complementary, not identical to the template strand. The result of this side's discontiguous replication is the production of a series of short sections of new DNA called Okazaki fragments (after their discoverer, a Japanese researcher). To make sure that this new strand of short segments is made into a continuous strand, the sections are joined by the action of an enzyme called DNA ligase which LIGATES the pieces together by forming the missing phosphodiester bonds!

The last step is for an enzyme to come along and remove the existing RNA primers (you don't want RNA in your DNA now that the primers have served their purpose, do you?) and then fill in the gaps with DNA. This is the job of yet another type of DNA polymerase which has the ability to chew up the primers (dismantle them) and replace them with the deoxynucleotides that make up DNA. Here is a link with a diagram of the overall process of DNA replication of Okazaki Fragments.

Since each new strand is complementary to its old template strand, two identical new copies of the DNA double helix are produced during replication. In each new helix, one strand is the old template and the other is newly synthesized, a result described by saying that the replication is semi-conservative. This process is shown schematically below. Crick described the DNA replication process and the fitting together of two DNA strands as being like a hand in a glove. The hand and glove separate, a new hand forms inside the old glove, and a new glove forms around the old hand. As a result, two identical copies now exist.

The process of DNA replication in all organisms is amazing, but in humans it seems particularly difficult to conceive. The sum of all genes in a human cell-the human genome-is estimated to be approximately 3 billion base pairs, and a single DNA chain might contain up to 250 million pairs of bases. What's even more incredible is how few mistakes are made in this process despite the immense size of human DNA! An error occurs only about once in each 10-100 billion bases. As you would probably expect, the complete process of DNA replication in human cells takes several hours. To replicate such huge molecules as human DNA at this speed requires not one, but many replication forks, forming replication bubbles and producing many segments of DNA strands that eventually meet up together and are joined to form the newly synthesized double helix.

Nucleic Acids And Heredity

NUCLEIC ACIDS AND HEREDITY

How is genetic information passed on from generation to generation, or just cell to cell? How can a "bunch of letters" determine what proteins are made in the cell and direct the cell's activities?

A mechanism must exist for copying DNA in a fool-proof manner. If the information is to be used, mechanisms must exist for decoding the information held in the sequence of "letters" and for carrying out the instructions coded in that sequence.

According to what has been called the central dogma of molecular genetics, the function of DNA is to store information and pass it on to RNA, while the function of RNA is to read, decode and use the information received from DNA to make proteins.

Three fundamental processes take place in the transfer and use of genetic information:

	1		Replication is the process by which a replica, or identical copy, of DNA is made. Replication occurs every time a cell divides so that information can be preserved and handed down to offspring. This is similar to making a copy of a file onto a disk so you can take that file to a different computer.
	2		Transcription is the process by which the genetic messages contained in DNA are "read" or transcribed. The product of transcription, known as messenger RNA (mRNA), leaves the cell nucleus and carries the message to the sites of protein synthesis. This tutorial explains later why this step is necessary in organisms with a nucleus!
	3		Translation is the process by which the genetic messages carried by mRNA are decoded and used to build proteins.

The important point to remember is that the processes outlined above do not necessarily have to take place in that exact order all the time. For instance, if you eat a bagel with cream cheese, and the specialized cells of your pancreas need to secrete a digestive enzyme, then the one gene for that enzyme will be transcribed from DNA to mRNA and then to the protein (the digestive enzyme) which will be released into the digestive tract to do its work. Does the cell need to replicate (copy) its DNA for this? NO!! The only reason a cell has for replicating its DNA is if it's going to divide (make new cells). If the cell simply wants to make a protein for day-to-day functions, then DNA replication is not necessary.

THE STRUCTURE OF NUCLEIC ACID CHAINS

THE STRUCTURE OF NUCLEIC ACID CHAINS

Nucleotides are joined together in DNA and RNA by phosphate ester bonds between the phosphate component of one nucleotide and the sugar component of the next nucleotide. An ester bond is a bond which occurs between a Carbon atom and an Oxygen atom.

More and more nucleotides can be added on by the same process of forming ester bonds until an immense chain is formed. But no matter how long a polynucleotide chain is, one end of the nucleic acid molecule always has a free -OH group on the sugar at the Carbon known as C3' (called the 3' end) and the other end of the molecule always has a phosphoric acid group at C5' (the 5' end). The Carbons get this name from a counting system illustrated in the next diagram.

Beginning from the "right-hand" side of the sugar, count the Carbons....1', 2', 3' (where the phosphate group of the next nucleotide in a series can be linked via a chemical bond), 4', 5' (where the phosphate group of the previous nucleotide is linked via a chemical bond).

This "counting system" allows the strand of nucleic acid to be oriented: the 5' end of the molecule always ends with a phosphate and the 3' end of the strand always ends with a sugar. You may be wondering why we don't just call the 5' end the "top" of the DNA or RNA molecule and the 3' end the "bottom" of the molecule. But in order to name something the "top", we're assuming that that end of the molecule is "up".

But how can you assume this in a cell?

YOU CAN'T! Remember that cells don't have specific orientations and that the nucleic acid within the cells is tightly wrapped and coiled around special proteins in the nucleus. So the terms "top" and "bottom" or "left" and "right" are pretty useless in this situation. Any nucleotides in between the 3' and 5' nucleotides would be involved in phosphodiester bonds. These nucleotides on the ends of each strand have a "free" end which is not involved in such a bond.

Click here to see one interpretation of the general structure of the nucleic acid DNA. The phosphate groups joined to sugar groups form what is known as the "backbone" of a nucleic acid molecule. The bases are attached to the sugars at a different point than the phosphate groups to form this generalized structure. The shape of DNA (a double-stranded molecule) is often referred to as a "double helix" or "twisted ladder" with the sugar-phosphate backbone forming the sides of the ladder and the nitrogen bases forming the rungs of the ladder in the middle.

The sequence of nucleotides in a chain is described by starting at the 5' end and identifying the bases in the order that they are linked together. Rather than write the full name of each nucleotide or each base, however, it's quicker and easier to use the simple one-letter abbreviations of the bases: A for Adenine, G for guanine, C for cytosine, T for thymine (and U for uracil in RNA). So, to describe a sequence of DNA, you might write something like -T-A-G-G-C-T-.

In the coming sections of this tutorial and in lecture, you will learn that the exact structure of a protein depends on the sequence in which the individual amino acids are connected. The same is true with nucleic acids; the exact structure of a nucleic acid molecule depends on the sequence in which individual nucleotides are connected. We'll return to this concept later in the tutorial.

NUCLEOTIDES

NUCLEOTIDES

The nucleotides that are the building blocks of nucleic acids are formed by adding a phosphate group to a nucleoside.



Nucleotides containing ribose are known as ribonucleotides, and those containing deoxyribose are known as deoxyribonucleotides.

To summarize the structural differences between DNA and RNA:

DNA (deoxyribonucleic acid)

• Sugar is deoxyribose
• DNA is a polymer of deoxyribonucleotides
• Bases are adenine, guanine, cytosine and thymine

RNA (ribonucleic acid)

• Sugar is ribose
• RNA is a polymer of ribonucleotides.
• Bases are adenine, guanine, cytosine and uracil (instead of thymine)

NUCLEOSIDES

NUCLEOSIDES

Both DNA and RNA contain nucleotides with similar components. In RNA, the sugar component is ribose, as indicated by the name "ribonucleic acid". In DNA, or deoxyribonucleic acid, the sugar component is deoxyribose. The prefix deoxy means that an oxygen atom is missing from one of the ribose Carbon atoms.

When a sugar bonds together with a Nitrogen base, you now have two of the three components of a nucleotide. This structure is known as a nucleoside.

There are FIVE Nitrogen bases that are found in DNA and RNA (although Uracil is found ONLY in RNA!). These five bases are divided into two categories based on their molecular structure. Click onto the hyperlinks and look at the structures below to see if you can tell what differentiates each category!

1 purines (Adenine and Guanine)
2 pyrimidines (Thymine, Cytosine, and Uracil)



You should notice that the purines have two ring structures while pyrimidines have only one ring structure. The way I've always remembered the difference is that the LONGER word (pyrimidine) represents the SMALLER structure (only one ring), and vice-versa!

COMPOSITION OF NUCLEIC ACIDS

COMPOSITION OF NUCLEIC ACIDS

This section of the tutorial begins to look at the composition of nucleic acids starting from the biggest subunit and going all the way down to the very chemical elements that make them up.

Nucleic acids are one of several macromolecules in the body in addition to fats, proteins and carbohydrates. So it isn't surprising that nucleic acids are built like these other macromolecules. Nucleic acids and the other macromolecules just mentioned are polymers made up of individual molecules linked together in long chains.

• Proteins are polypeptides made up of individual amino acids linked together,
• Carbohydrates are polysaccharides made up of individual monosaccharides linked together, and
• Nucleic acids are polynucleotides made up of individual nucleotides linked together.

If you go even further, a nucleotide can itself be further broken down to yield three components:

• a sugar,
• a Nitrogen (amine) base, and
• phosphoric acid.
  

As mentioned in the Introduction to this tutorial, there are two types of nucleic acids: DNA and RNA. DNA stores genetic information, and RNA allows that information to be made use of in the cell. Before we discuss the overall structure of nucleic acids as polymers, we should probably find out how their individual component parts are joined together and how DNA and RNA differ.

Physical and chemical properties-DNA

Physical and chemical properties

DNA is a long polymer made from repeating units called nucleotides.[1][2] The DNA chain is 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit is 3.3 Å (0.33 nm) long.[3] Although each individual repeating unit is very small, DNA polymers can be enormous molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long.[4]

In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules.[5][6] These two long strands entwine like vines, in the shape of a double helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. In general, a base linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. If multiple nucleotides are linked together, as in DNA, this polymer is called a polynucleotide.[7]

The backbone of the DNA strand is made from alternating phosphate and sugar residues.[8] The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand. This arrangement of DNA strands is called antiparallel. The asymmetric ends of DNA strands are referred to as the 5′ (five prime) and 3′ (three prime) ends. One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA.[6]

The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.

These bases are classified into two types; adenine and guanine are fused five- and six-membered heterocyclic compounds called purines, while cytosine and thymine are six-membered rings called pyrimidines.[6] A fifth pyrimidine base, called uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine.

Major and minor grooves

The double helix is a right-handed spiral. As the DNA strands wind around each other, they leave gaps between each set of phosphate backbones, revealing the sides of the bases inside (see animation). There are two of these grooves twisting around the surface of the double helix: one groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide.[10] The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove

Deoxyribonucleic Acid (DNA)

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.

Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.