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Biology library
Course: Biology library > Unit 21
Lesson 1: More about DNA and RNA- DNA and RNA structure
- Introduction to nucleic acids and nucleotides
- Molecular structure of RNA
- Antiparallel structure of DNA strands
- Semi conservative replication
- DNA structure and replication review
- Replication
- The genetic code
- DNA and chromatin regulation
- Intro to gene expression (central dogma)
- Cellular specialization (differentiation)
- Eukaryotic gene transcription: Going from DNA to mRNA
- Regulation of transcription
- Transcription and RNA processing
- Non-coding RNA (ncRNA)
- Regulation of gene expression and cell specialization
- Post-transcriptional regulation
- Translation
- Differences in translation between prokaryotes and eukaryotes
- Prokaryote structure
- Retroviruses
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DNA structure and replication review
Key terms
| Term | Meaning |
|---|---|
| DNA (deoxyribonucleic acid) | Nucleic acid that transmits genetic information from parent to offspring and codes for the production of proteins |
| Nucleotide | Building block of nucleic acids |
| Double helix | Structure of two strands, intertwining around an axis like a twisted ladder |
| DNA replication | Process during which a double-stranded DNA molecule is copied to produce two identical DNA molecules |
| Base pairing | Principle in which the nitrogenous bases of the DNA molecules bond with one another |
DNA structure
DNA is a nucleic acid, one of the four major groups of biological macromolecules.
Nucleotides
All nucleic acids are made up of nucleotides. In DNA, each nucleotide is made up of three parts: a 5-carbon sugar called deoxyribose, a phosphate group, and a nitrogenous base.
DNA uses four kinds of nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).
RNA nucleotides may also contain adenine, guanine and cytosine bases, but instead of thymine they have another base called uracil (U).
Chargaff's rules
In the 1950s, a biochemist named Erwin Chargaff discovered that the amounts of the nitrogenous bases (A, T, C, and G) were not found in equal quantities. However, the amount of A always equalled the amount of T, and the amount of C always equalled the amount of G.
These findings turned out to be crucial to uncovering the model of the DNA double helix.
Double helix
The discovery of the double helix structure of DNA was made thanks to a number of scientists in the 1950s.
DNA molecules have an antiparallel structure - that is, the two strands of the helix run in opposite directions of one another. Each strand has a 5' end and a 3' end.
Solving the structure of DNA was one of the great scientific achievements of the century.
Knowing the structure of DNA unlocked the door to understanding many aspects of DNA's function, such as how it is copied and how the information it carries can be used to produce proteins.
DNA replication
DNA replication is semi-conservative. This means that each of the two strands in double-stranded DNA acts as a template to produce two new strands.
Replication relies on complementary base pairing, that is the principle explained by Chargaff's rules: adenine (A) always bonds with thymine (T) and cytosine (C) always bonds with guanine (G).
The replication process
DNA replication occurs through the help of several enzymes. These enzymes "unzip" DNA molecules by breaking the hydrogen bonds that hold the two strands together.
Each strand then serves as a template for a new complementary strand to be created. Complementary bases attach to one another (A-T and C-G).
The primary enzyme involved in this is DNA polymerase which joins nucleotides to synthesize the new complementary strand. DNA polymerase also proofreads each new DNA strand to make sure that there are no errors.
Leading and lagging strands
DNA is made differently on the two strands at a replication fork.
One new strand, the leading strand, runs 5' to 3' towards the fork and is made continuously.
The other, the lagging strand, runs 5' to 3' away from the fork and is made in small pieces called Okazaki fragments.
Example: Determining a complementary strand
DNA is only synthesized in the 5' to 3' direction. You can determine the sequence of a complementary strand if you are given the sequence of the template strand.
For instance, if you know that the sequence of one strand is 5’-AATTGGCC-3’, the complementary strand must have the sequence 3’-TTAACCGG-5’. This allows each base to match up with its partner:
Common mistakes and misconceptions
- DNA replication is not the same as cell division. Replication occurs before cell division, during the S phase of the cell cycle. However, replication only concerns the production of new DNA strands, not of new cells.
- Some people think that in the leading strand, DNA is synthesized in the 5’ to 3’ direction, while in lagging strand, DNA is synthesized in the 3’ to 5’ direction. This is not the case. DNA polymerase only synthesizes DNA in the 5’ to 3’ direction only. The difference between the leading and lagging strands is that the leading strand is formed towards replication fork, while the lagging strand is formed away from replication fork.
Want to join the conversation?
What is the difference between:
Replication fork
Replication complex
Replication unit
Origin of replication
Replication bubble(10 votes)
The replication fork is the branched (forked) DNA at either end of the replication bubble.
The replication complex is the group of proteins that help synthesize the new DNA strands.
A replication unit is any chunk of DNA that is capable of being replicated — e.g. a plasmid with an origin of replication (ORI) is a replication unit. Alternatively, this can also mean a region of DNA that is replicated together.
An ORI is a DNA sequence at which replication is initiated. ORIs are recognized by the replication machinery — specifically the pre-replication complex.
A replication bubble is the region of DNA where new strands of DNA have been or are being synthesized. A replication fork is found at each end of a replication bubble.
You can find more details and (many) of these terms in this free online book chapter:
https://www.ncbi.nlm.nih.gov/books/NBK26826/
This seems like a reasonable source for quick definitions of terms:
http://dictionary.sensagent.com/(26 votes)
What does it mean to have a 3' end as opposed to a 5' end?(7 votes)
5' ends with the phosphate, and 3' ends with the deoxyribose sugar.(14 votes)
Baby don't hurt me...(2 votes)
- lagging strand how to memorize it(4 votes)
leading strand synthesized continually whereas lagging strand is synthesized in fragments(Okazaki fragments)
Memorize it this way: Lagging strand lags behind and does his homework(replicating dna) in bursts when he feels like it. Leading strand leads the way and is a good model. lol(7 votes)
isnt the leading and lagging strand different because when unzipping the DNA the halfs are pointing in oppisite directions of one another?(5 votes)
yes the leading strand goes towards the replication fork and the lagging strand goes away from the replication fork in okazaki fragments(5 votes)
- 1-Unwinding the (origin of replication) is done when certain proteins are attached to the site (which is AT rich) , I mean not by Helicase , right?
2-who removers the primers in the lagging strand?
Is it the same DNA pol ?
3-Why does polymerization rate in prokaryotes is faster than in eukaryotes?(4 votes)- 1) My understanding is that many proteins are involved in unwinding the origin of replication including at least one helicase.
Note that helicase is a type of activity, not a single protein — for examples and more details see:
https://en.wikipedia.org/wiki/Helicase
2) The primer is removed by an endonuclease that recognizes RNA:DNA hybrids (RNase H) and then exonucleases that remove the RNA nucleotides. In E. coli this exonuclease activity is performed by DNA polymerase I.
3) Eukaryotic DNA is generally much longer, more complex (typically multiple linear chromosomes with ends vs. usually circular DNA), and is highly packaged into nucleosomes (and higher order structures). All of these factors mean that it takes longer to replicate eukaryotic DNA.
References and further reading:
https://www.ncbi.nlm.nih.gov/books/NBK9940/
https://sydney.edu.au/science/molecular_bioscience/PHAR2811/PHARlectures/PHARlecture5/PHARlecture5notes.pdf(3 votes)
- which enzyme breaks the h bonds?(3 votes)
As enzymes breaks the hydrogen bonds that hold the double helix together,so the two strands unwind and separate and that enzymes is helicase(5 votes)
- is there any case in which primer exist in DNA after replication(3 votes)
Usually, there is not because DNA Polymerase always replaces the RNA nucleotides with the DNA nucleotides. Unless for some reason, the DNA Polymerase fails to function, it may happen but proofreading should catch it. Otherwise, there should not be any errors.(4 votes)
What really are Okazaki fragments(3 votes)
They are the replicated parts of the lagging strand. The DNA can only be replicated/translated in one direction, so it goes the right way in short fragments. Those fragments are called Okazaki fragments.(4 votes)
