Biological Roles of DNA & RNA, Replication, Transcription & Translation

Biological Roles of DNA & RNA, Replication, Transcription & Translation

DNA:

(deoxyribonucleic acid) is one of the most important molecules in your body, and though around 99.9% of your DNA is the same as that of every other human, the 0.1% that’s different is what makes you genetically unique! This tiny biological structure is the ultimate instruction manual, containing the “recipes” for the proteins your body needs to develop and function. 

Today, we’re going to give you a primer on the basics of DNA. We’ll talk about its structure, how it replicates, and the role it plays in the production of proteins. 

One monomer unit = deoxyribonucleic acid 

• composed of a base, a sugar (deoxyribose), and a phosphate 

• directionality along the backbone
5’ (phosphate) to 3’ (OH) 

Double-strand pairing: 

• complementary base-matching: A-T, C-G 

• base-matching achieved by H-bonding and geometry (long vs short nucleotides) 

• antiparallel (one strand 5’
3’, the other 3’
5’) 

Helical shape 

• 10.4 nucleotides per turn 

• diameter = 2 nm 

• both major and minor grooves 

• called B-DNA. The helix twist and diameter can also change under dehydrating 

conditions and methylation to A-DNA and Z-DNA

Base-pairing and strand interactions 

• A, G are long (double ring purines) 

• C,T are short (single ring pyrimidines) 

• need one long and one short nucleotide per pair 

• C-G have three hydrogen bonds (slightly stronger matching) 

• A-T have two hydrogen bonds (slightly weaker matching) 

• base stacking of aromatic rings allows sharing of pi electrons and adds stability to 

interior structure of DNA
some hydrophobic driving force as well 

• pair structure allows template for semi-conservative copying

Information in DNA sequence is the genome

• genes are stretches of information in the sequence that encode for particular function 

(usually a particular protein, but sometimes also an RNA sequence) 

• about 20,000 genes in humans 

• typically 1000s of nucleotides long 

• genes can be expressed (use to make proteins) or repressed (not used) 

• regions of DNA are divided into coding and non-coding segments 

• over 50% of human DNA is non-coding 

• genes can be spliced together 

• genes are organized in the large-scale structure of the DNA in the nucleus 

In bacteria, genome usually circular 

The genome in eukaryotes is organized into chromosomes

• each chromosome a separate DNA molecule 

• human cells contain 46 chromosomes (22 each from mother and father) 

• chromosomes are extended and replicated during interphase portion of the cell cycle

extended allows for gene expression 

• chromosomes are condensed, visible with light during cell division (M phase) 

Special DNA sequences exist in each chromosome 

• replication origins – multiple locations where the replication machinery first binds to 

start replication 

• centromere – center “pinch point” of a chromosome that allows one copy of each to be 

pulled apart into two daughter cells during division 

telomere – specialized sequences at the chromosomes end that facilitate replication 

there 

Higher-order DNA structure 

• How do cells efficiently store very long chains of DNA? 

• DNA wraps around protein “spools” to form nucleosomes

• Nucleosomes are made of histone proteins 

• Spools organize into chromatin fibers that pack in regular ways, on different length scales 

There are 46 separate strings of DNA in each somatic cell of the human body. Each one of these is called a chromosome. Scientists group them into 23 homologous pairs, which means that the chromosomes in each pair are similar in structure and function. The only exception to this is the 23rd pair—the sex chromosomes—in biologically male individuals. X and Y sex chromosomes only have certain regions (autosomal regions) that are homologous.  

At the molecular level, DNA has a characteristic double-helix shape, and though this wasn’t observed by scientists until mid-20th century, it has quickly become one of the most iconic shapes in all of science. 

The sides of this twisted ladder are composed of alternating molecules of sugar (deoxyribose, to be precise) and a phosphate group. Each side is named for the direction it runs in (5’–3’ or 3’–5’). The ladder’s “steps” are composed of two nitrogenous bases, held together with hydrogen bonds.

Molecular structure of DNA.

Four nitrogenous bases—cytosine, thymine, adenine, and guanine—can be found on strands of DNA. In terms of their chemical structure, cytosine and thymine are pyrimidines and adenine and guanine are purines. Adenine and thymine (A and T) always pair together, and guanine and cytosine (G and C) always pair together. They pair this way because A and T form two hydrogen bonds with each other and G and C form three. 

At the most basic level, different sections of DNA strands (sequences of nitrogenous bases) provide instructions for the synthesis of proteins. A single section of DNA can even code for multiple proteins!

RNA:

Ribonucleic acid (abbreviated RNA) is a nucleic acid present in all living cells that has structural similarities to DNA. Unlike DNA, however, RNA is most often single-stranded. An RNA molecule has a backbone made of alternating phosphate groups and the sugar ribose, rather than the deoxyribose found in DNA. Attached to each sugar is one of four bases: adenine (A), uracil (U), cytosine (C) or guanine (G). Different types of RNA exist in cells: messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA). In addition, some RNAs are involved in regulating gene expression. Certain viruses use RNA as their genomic material.

Ribonucleic acid, or RNA. I often think of RNA as being the less well-known cousin of DNA, particularly for people outside the field of biology or genomics. But really, when you think about it, RNA, in so many ways, is the actual functional form of nucleic acids that really the body uses to do the business of, you know, constructing cells or responding to immune challenges, of carrying amino acids from one part of the cell to the other, that quite often I feel that RNA doesn't get the respect it deserves. So what I think we can share is that the different forms of RNA -- mRNA, tRNA, rRNA -- each in their own way have absolutely fundamental functions without which the biology of the genome could not be translated into practice. And I guess the most obvious one here might be mRNAs, because these are the transcribed forms of genes, the form in which a gene gets read by the cell. But really, I would encourage everyone to learn about the unique roles that tRNAs and rRNAs have as well, because each of these fits into the puzzle of life in a wonderfully unique way.

 

Replication: Doubling Up on DNA

Illustration from A&P 6.

Replication of a cell’s DNA occurs before a cell prepares to undergo division—either mitosis or meiosis I.

It takes place in three(ish) steps.

1. DNA unwinds from the histones.
2. An enzyme called DNA helicase opens up the helix structure on a segment of DNA, breaking the bonds between the nitrogenous bases. It does this in a zipper-like fashion, leaving a replication fork behind it.
3. Here’s where things get funky. 
• On the 5’–3’ strand of the DNA, an enzyme called DNA polymerase slides towards the replication fork and uses the sequence of nitrogenous bases on that strand to make a new strand of DNA complementary to it (this means that its bases pair with the ones on the old strand). 
• On the 3’–5’ strand, multiple DNA polymerases match up base pairs in partial segments, moving away from the replication fork. Later, DNA ligase connects these partial strands into a new continuous segment of DNA.

Want to know something neat? When a DNA molecule replicates, each of the resulting new DNA molecules contains a strand of the original, so neither is completely “new."  Also, new histones are made at the same time the DNA replicates so that the new strands of DNA can coil around them.

 

Interlude: RNA vs DNA

Before we discuss transcription and translation, the two processes key to protein synthesis, we need to talk about another kind of molecule: RNA.

RNA is a lot like DNA—it’s got a sugar-phosphate backbone and contains sequences of nitrogenous bases. However, there are a couple of vital differences between RNA and DNA:

• RNA has only one nucleotide chain. It looks like only one side of the DNA ladder.

• RNA has ribose as the sugar in its backbone.

• RNA has Uracil (U) instead of thymine.

• RNA is smaller than DNA. RNA caps out at around 10,000 bases long, while DNA averages about 100 million.
• RNA can leave the nucleus. In fact, it does most of its work in the cytoplasm.

There are several different types of RNA, each with different functions, but for the purposes of this article, we’re going to focus on messenger RNA (mRNA) and transfer RNA (tRNA).

 

Making a Protein,  Transcription

Transcription is the first phase of the protein-making process, even though the actual protein synthesis doesn’t happen until the second phase. Essentially, what happens during transcription is that an mRNA “copies down” the instructions for making a protein from DNA.

Illustration from A&P 6.

First, an enzyme called RNA polymerase opens up a section of DNA and assembles a strand of mRNA by “reading” the sequence of bases on one of the strands of DNA. If there’s a C on the DNA, there will be a G on the RNA (and vice versa). If there’s a T on the DNA, there will be an A on the RNA, but if there’s an A on the DNA, there will be a U (instead of a T) on the RNA. As the RNA polymerase travels down the string of DNA, it closes the helical structure back up after it. 

Before the new mRNA can go out to deliver its protein fabrication instructions, it gets “cleaned up” by enzymes. They remove segments called introns and then splice the remaining segments, called exons, together. Exons are the sequences that actually code for proteins, so they’re the ones the mRNA needs to keep. You can think of introns like padding between the exons.

Also, remember how I mentioned that a single sequence of DNA can code for multiple proteins? Alternative splicing is the reason why: before the mRNA leaves the nucleus, its exons can be spliced together in different ways 

Making a Protein,  Translation

After it’s all cleaned up and ready to go, the mRNA leaves the nucleus and goes out to fulfill its destiny: taking part in translation, the second half of protein construction

In the cytoplasm, the mRNA must interface with tRNA with the help of a ribosome. tRNA is a type of RNA that has a place to bind to free amino acids and a special sequence of three nitrogenous bases (an anticodon) that binds to the ribosome.

Ribosomes are organelles that facilitate the meeting of tRNA and mRNA. During translation, ribosomes and tRNA follow the instructions on the mRNA and assemble amino acids into proteins. 

Each ribosome is made up of two subunits (large and small). These come together at the start of translation. Ribosomal subunits can usually be found floating around in the cytoplasm, but a ribosome will dock on the rough endoplasmic reticulum if the protein it’s making needs to be put into a transport vesicle. Ribosomes also have three binding sites where tRNA can dock: the A site (aminoacyl, first position), the P site (peptidyl, second position) and the E site (the exit position).

Ultimately, translation has three steps: initiation, elongation, and termination. 

During initiation, the strand of mRNA forms a loop, and a small ribosomal subunit (the bottom of the ribosome) hooks onto it and finds a sequence of bases that signals it to begin transcription. This is called the start codon (AUG).

Then, a tRNA with UAC anticodon pairs with this start codon and takes up the second position (P) site of the ribosome. This tRNA carries the amino acid Methionine (Met). At this point, the large ribosomal subunit gets in position as well (it’s above the mRNA and the small subunit is below).

In the elongation phase, the fully-assembled ribosome starts to slide along the mRNA. Let’s say the next sequence of bases it encounters after the start codon is GCU. A tRNA molecule with the anticodon CGA will bind to the first position (A) site of the ribosome. The amino acid it’s carrying (alanine) forms a peptide bond with Met. Afterward, the CGA tRNA (carrying the Met-Ala chain) moves to the second position and the UAC tRNA enters the E binding site. The first position site is then ready to accept a new tRNA. This process keeps going until the ribosome gets to a “stop” codon.

Termination is pretty much what it sounds like. Upon reaching the “stop” codon, the tRNA that binds to the first position carries a protein called a release factor. The amino acid chain then breaks off from the ribosome, either going off into the cytosol or into the cisterna of the rough ER, and the ribosome disassembles. However, it might very well reassemble and go around the mRNA loop again. Also, multiple ribosomes can work on the same mRNA at once!

And those are the basics of DNA! 

Here’s a handy chart you can look at if you need to remember the differences between transcription, translation, and replication: 

	Location	Purpose	Main Participants	Product(s)
Replication	Nucleus	Duplicate a full strand of DNA	DNA DNA helicase DNA polymerase DNA ligase	2 identical strands of DNA
Transcription	Nucleus	Use a strand of DNA to build a molecule of mRNA	DNA RNA polymerase (DNA ligase)	mRNA
Translation	Cytoplasm	Use mRNA to build an amino acid chain	mRNA Ribosome tRNA (and amino acids)	Amino acid chain (protein)