Table of Contents
Learning Objective
By the end of this lecture, you should be able to fully describe DNA, the structure of a DNA and its component functions, how DNA is replicated and transcribed. Remember, you are to go nowhere if you are not able to score upto 70% in the quiz.
Introduction
Deoxyribonucleic Acid (DNA) contains the information for life – all the instructions needed to make proteins (including enzymes).
A segment of DNA that controls the production of a protein is called a GENE.
Hundreds of genes together make up a chromosome.
DNA > Gene > chromosome
DNA structure
DNA is found primarily in the nucleus of eukaryotic cells and in the nucleoid of bacteria.
Because the cell is so small, DNA is usually packed into a compact form called CHROMATIN. Small amounts of DNA are also found in organelles (such as mitochondria and chloroplasts) that contain their own genomes, in autonomously maintained DNAs called plasmids, and in viruses.
DNA is composed of two long polymer strands of:
- Sugar: 2-deoxyribose.
- Phosphate.
- Purine and Pyrimidine bases.
The backbone of each strand is composed of alternating 2-deoxyribose and phosphate linked together through phosphodiester bonds.
The four bases found in DNA are:
- Adenine
- Thymine
- Guanine
- Cytosine.
Each 2-deoxyribose is linked to one of the four bases via a covalent glycosidic bond.
A base linked to a sugar is called a nucleoside, and a base linked to a sugar phosphate is called a nucleotide.
The sequence of these four bases allows DNA to carry genetic information.
Bases can form hydrogen bonds with each other.
Adenine forms two bonds with thymine, and cytosine forms three bonds with guanine.
These two sets of base pairs have the same geometry, allowing DNA to maintain the same structure regardless of the specific sequence of base pairs.
For cells to live and grow, the genetic information in DNA must be:
- Propagated and maintained from generation to generation.
- Expressed to synthesize the components of a cell.
These two functions are carried out by the processes of DNA replication and transcription, respectively.
DNA Replication
DNA replication is the process of duplicating a cell's genome. It is required every time a cell divides.
DNA replication occurs during the S-phase of interphase.
How does DNA replicate?
Stage 1: PreReplication [Formation of Replication Fork]
Before DNA can be replicated, the double strands must be unzipped into two single strands.
Like I said earlier, DNA has four bases called adenine [A], thymine [T], cytosine (C) and guanine (G). These four bases are the ones responsible for the joining together of two single strands to form a double strand.
These bonds (hydrogen bonds) must be broken to unzip the DNA.
This unzipping process is performed by an enzyme known as Helicase.
Helicase breaks the hydrogen bonds between these bases, and as a result the two strands are now separated.
After the DNA has been unzipped, the double strands are now stand-alone strands (they are no longer joined together) and they form a Y shape called a Replication Fork.
The two separated strands will now act as template where new strands will attach to form two new DNAs.
One Important thing you should know: DNA direction
DNA is read in direction, just as you are reading this post from left to right.
Now, if we read from left to right, we also read DNA either from 3' to 5' direction or 5' to 3' direction. This is pronounced as 3 prime to 5 prime direction or 5 prime to 3 prime direction.
What is 3 prime and 5 prime direction?
3 prime and 5 prime direction, I love calling them markings. Like, they are important points on a DNA strand.
If you remember I said earlier that DNA is a long polymer of deoxyribose sugar (plus others). This sugar has carbon atoms that are marked as 1,2,3,4,5...
I don't want to go far therefore I will be discussing within our context only:
On this fifth carbon atom (called 5' / 5 prime), a phosphate group (P) is attached to it.
While on the third carbon atom (called 3' / 3 prime), an hydroxyl group (OH) is attached to it.
Like I said, these are two separate markings. If I say from 3' to 5' direction, I mean that we are reading up... And if I say 5' to 3' direction, I mean that we are reading / writing down...
If you do not get that explanation on DNA direction I would want you to watch the video below.
I hope you're following me?
Now let us move on.
When a Replication Fork is formed, two single strands are formed.
One moves towards the replication fork (3' to 5' direction) and it is called Leading strand.
The other moves away from the replication fork (5' to 3' direction) and it is called lagging strand.
These two strands are then replicated using two different processes.
Stage 2: Replication [Replication of Leading strand and Lagging strand]
Replication of the leading strand and lagging follow different processes.
Replication of Leading Strand
While the leading strand from the Replication Fork stays on its own, nothing happens. Until a short piece of RNA called Primer comes to bind to the 3 prime (3') end of the strand.
Primer is produced by an enzyme called Primase.
Primer always binds at the starting point of the leading strand for replication.
Primer binding begins the replication process.
After the primer is done binding with the leading strand, another enzyme known as DNA polymerase comes to attach to the leading strand at the site of the primer.
This polymerase starts to walk along the leading strand. Polymerase walks along the leading strand in the 5' to 3' direction (opposite the orientation of the leading strand).
All DNA polymerase:
- Synthesize new DNA in a 5′ to 3′ direction.
- Require a primer (they must add on to the 3′ hydroxyl position of DNA or RNA)
- Require a DNA molecule as a template.
As it is walking along the leading strand, it is adding new base pairs (C, G, A, T) that bonds with the leading strand complementarily.
This type of replication is called Continuous and it occurs very fast.
Replication of Lagging Strand
The lagging strand moves in a direction that is opposite the replication fork and leading strand (i.e, it moves in 5' to 3' direction).
In the lagging strand, many Primers from the Primase enzyme attach to it at several points, each are a few distances apart from the other.
DNA polymerase also comes here and moves in a 5' to 3' direction (same direction as the leading strand) but here it adds short pieces of DNA in between the primers (technically, this is because the primers are actually blocking the way if it was to walk straightforwardly. LOL).
These short pieces of DNA are called Okazaki Fragments and what is in between two Okazaki fragments is a primer.
This process of replication is discontinuous because the new DNA (Okazaki fragments) are not joined.
Stage 3: Primers Removal
Once both the continuous and discontinuous strands are fully formed, an enzyme known as Exonuclease comes and removes all Primers from the original strands. The gaps left by these primer(s) are then filled with appropriate bases.
In the continuous strand, there's only one gap which is filled up, but in discontinuous strands, there are numerous gaps between each Okazaki fragments.
Another enzyme called DNA Ligase finally joins Okazaki fragments together forming a single unified strand.
Stage 4: Final Wrap up [Addition of Telomere]
Everything should have been wrapped up in the previous stage, but no, we are not done yet. There's still a problem:
The ends of parent strands (leading strand and lagging strand) consist of repeated DNA sequences called Telomeres.
Telomere act as protective cap at the end of DNA to prevent nearby DNA from fusing.
A special type of DNA polymerase enzyme called telomerase catalyzes the formation of new Telomeres at the end of the newly formed DNA.
Stage 5: Recoil back into Double Helix
This is the final stage in DNA replication.
Each parent strand (leading strand and Lagging Strand) and its new complementary DNA strands coils into the familiar double helix shape.
In the end, replication yields two new DNA molecules, each with one strand from the parent molecule and one new strand. This is the reason why DNA replication is always referred to as Semi-Conservative.
DNA Transcription — Making mRNA
DNA transcription involves the expression of DNA to synthesize the components of a cell.
In DNA transcription, DNA is re-written into messenger RNA (mRNA) by RNA polymerase.
DNA transcription almost follows the same process as DNA replication, just some differences.
How is DNA transcribed
The process of DNA transcription is divided into three main stages:
- Initiation.
- Elongation.
- Termination.
Initiation
Initiation is the beginning of DNA transcription.
Here, an enzyme called RNA polymerase walks along the DNA until it recognizes a promoter sequence.
This promoter sequence is the area of DNA that indicates the starting point of transcription.
At this point (promoter sequence), signal is sent to the DNA to unwind (separate the bonded base pairs).
The enzyme then reads up one of the two different strands (which is the template strand or antisense strand) of the DNA in the 3' to 5' direction (like we discussed previously) and starts getting ready to write it down in the 5' to 3' direction, that is, attach each bases to its complement.
Elongation
The template strand which has been read up is now written down to form a new strand. This new strand is RNA strand or molecule and it is composed of Ribose sugar (as opposed deoxyribose sugar in DNA).
While the DNA strands are written down, adenine complements thymine, cytosine complements guanine, guanine complements cytosine, and uracil complements adenine.
You see the difference here?
While we were discussing DNA replication, in the writing down of strands, adenine is attached to thymine, cytosine is attached to guanine, guanine is attached to cytosine and thymine is attached to adenine.
But in transcription, instead of thymine to attach to adenine, uracil is now the one attached.
Termination
Elongation (formation of mRNA strands) continues until the RNA polymerase encounters a stop (termination) sequence. At this point, the mRNA strand is complete and it detaches from the DNA.
After the RNA has been detached, the DNA is closed back up.
The mRNA which has been transcribed up to this point is referred to as pre-mRNA.
Processing must occur to convert this into mature mRNA.
Processing of pre-mRNA to give a mature mRNA
This processing involves the addition of a cap and a tail to the mRNA molecule to make it more stable. The useless non-coding regions are also cut off during this processing. The processes are carefully explained below:
5' (5 prime) capping
This describes the addition of a methylated guanine cap to the 5 prime end of mRNA.
This is important because it is part of what will be recognized by Ribosomes for translational processes. It also protect the pre-mRNA from break down by RNAases.
Polyadenylation
This describes the addition of poly(A) tail to the 3 prime end of the pre-mRNA. This stabilises the molecule since RNA is very much unstable than DNA.
Splicing
Look at the name, splicing, it has defined itself.
Splicing is basically the removal of the non-coding region of mRNA (called introns) and the remaining regions which is the coding region (called exons) are stitched back together.
Removal of introns (non-coding sequences) is carried out via spliceosome excision.
Joining together of exons (coding sequences) is carried out via Ligation.
By the end of transcription, mature mRNA has been made.
mRNA acts as the messaging system to allow translation and protein synthesis to occur.
In our next discussion, we shall be talking on Translation of mRNA.
This is DNA review. DNA will be fully discussed in AGR 203 and beyond.
Summary
☑️DNA stands for Deoxyribonucleic Acid.
☑️DNA is found primarily in the nucleus of eukaryotic cells and in the nucleoid of bacteria.
☑️A segment of DNA that controls the production of a protein is called a gene.
☑️DNA is composed of two long polymer strands of:
- Sugar: 2-deoxyribose.
- Phosphate.
- Purine and Pyrimidine bases.
☑️The four bases found in DNA are adenine, thymine, guanine, and cytosine.
☑️These bases attach in pairs by hydrogen bonds (A to T, C to G).
☑️Each 2-deoxyribose is linked to one of the four bases via a covalent glycosidic bond.
☑️For cells to live and grow, the genetic information in DNA must be:
- Propagated and maintained from generation to generation.
- Expressed to synthesize the components of a cell.
☑️These two functions are carried out by the processes of DNA replication and transcription, respectively.
☑️DNA replication is the process of duplicating a cell's genome.
☑️DNA replication involves 5 stages:
Stage 1: PreReplication [Formation of Replication Fork]
Stage 2: Replication [Replication of Leading strand and Lagging strand]
Stage 3: Primers Removal
Stage 4: Final Wrap up [Addition of Telomere]
Stage 5: Recoil back into Double Helix
☑️DNA transcription involves the re-writing of DNA into mRNA.
☑️The process of DNA transcription is divided into three main stages:
- Initiation.
- Elongation.
- Termination.
☑️The end product of transcription known as pre-mRNA needs to be further modified by adding two bases to each ends to make the RNA molecule stable and recognized by Ribosomes. Inactive parts are also cut out.
Recommended Videos
Test Questions
TEST: DNA REVIEW
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TEST: DNA REVIEW
Total Questions: 30
you'll have 30 second to answer each question.
Quiz Result
Total Questions:
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Percentage:
Quiz Answers
1. In which direction is the mRNA transcript made during transcription
5' to 3'
2. Which enzyme catalyzes transcription?
RNA polymerase
3. Which base is not present in RNA
Thymine
4. Which base is not present in DNA?
Uracil
5. Which sugar is present in DNA?
Deoxyribose
6. What is transcription?
How DNA is converted to RNA
7. Which of these is cut out from mRNA during splicing?
Intron
8. _ enzyme joins the several Okazaki fragments on a lagging strand together
Ligase
9. DNA polymerase walks along the
5' to 3' direction
10. Short pieces of DNA attached to the lagging strand by DNA polymerase are called?
Okazaki Fragments
11. What is attached to the 5th carbon atom of DNA's deoxyribose sugar?
Phosphate group
12. What is attached to the 3rd carbon atom of DNA's deoxyribose sugar molecule?
Hydroxyl group
13. DNA replication occurs during
Interphase
14. The unzipping or unwinding of DNA is aided by what enzyme?
Helicase
15. Primers are produced by _
Primase
16. Replication on the leading strand is _
Continuous
17. Replication on the Lagging strand is _
Discontinuous
18. Cytosine base forms hydrogen bond with
Guanine
19. _ enzyme removes all Primers from the original strands
Exonuclease
20. Repeated DNA sequences at the ends of parent strands is called?
Telomere
21. Telomere formation on new strands is catalysed by _
Telomerase
22. DNA replication is _
Semi-conservative
23. DNA transcription will only start when the RNA polymerase has identified the _
Promoter sequence
24. DNA fully means
Deoxyribonucleicacid
25. The base pairs in DNA molecule are joined together by _
Hydrogen bonds
26. DNA transcription occurs in _ of eukaryotic cell
Nucleus
27. Inside a cell, DNA is packed into a compact form called
Chromatin
28. Backbone of DNA strands: Alternating 2-deoxyribose and phosphate, are linked together by _
Phosphodiester bond
29. The segment of DNA that controls the production of protein is called
Gene
30. DNA replication takes place in the _
Nucleus
