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DNA structure and replication review

AP.BIO:
IST‑1 (EU)
,
IST‑1.M (LO)
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IST‑1.M.1 (EK)

Key terms

TermMeaning
DNA (deoxyribonucleic acid)Nucleic acid that transmits genetic information from parent to offspring and codes for the production of proteins
NucleotideBuilding block of nucleic acids
Double helixStructure of two strands, intertwining around an axis like a twisted ladder
DNA replicationProcess during which a double-stranded DNA molecule is copied to produce two identical DNA molecules
Base pairingPrinciple 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.
Image of a DNA double helix, illustrating its right-handed structure. The major groove is a wider gap that spirals up the length of the molecule, while the minor groove is a smaller gap that runs in parallel to the major groove. The base pairs are found in the center of the helix, while the sugar-phosphate backbones run along the outside.
DNA double helix. Image modified from OpenStax, CC BY 3.0.
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

Semi-conservative replication produces two helices that contain one old and one new DNA strand.
Semi-conservative replication. Image modified from OpenStax, CC BY 3.0.
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

Schematic of Watson and Crick's basic model of DNA replication.
  1. DNA double helix.
  2. Hydrogen bonds break and helix opens.
  3. Each strand of DNA acts as a template for synthesis of a new, complementary strand.
  4. Replication produces two identical DNA double helices, each with one new and one old strand.
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).
DNA template strand and the creation of its complementary strand
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.
Diagram of leading and lagging replication strands

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:
5'-AATTGGCC-3' 3'-TTAACCGG-5'
These two strands are complementary, with each base in one sticking to its partner on the other. The A-T pairs are connected by two hydrogen bonds, while the G-C pairs are connected by three hydrogen bonds.

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?

  • blobby green style avatar for user Manar Al-Masri
    What is the difference between:
    Replication fork
    Replication complex
    Replication unit
    Origin of replication
    Replication bubble
    (8 votes)
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    • female robot grace style avatar for user tyersome
      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/
      (18 votes)
  • duskpin seed style avatar for user Arman
    What does it mean to have a 3' end as opposed to a 5' end?
    (5 votes)
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  • blobby green style avatar for user Ashwani Kumar
    is there any case in which primer exist in DNA after replication
    (3 votes)
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    • male robot hal style avatar for user prnvkumar
      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.
      (3 votes)
  • blobby green style avatar for user Manar Al-Masri
    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?
    (3 votes)
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  • blobby green style avatar for user tanishdeep dhanju
    which enzyme breaks the h bonds?
    (2 votes)
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  • blobby green style avatar for user Joanna Njeri
    How much of the original DNA molecule is found in each one of the new DNA molecule?
    (3 votes)
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  • female robot ada style avatar for user Maha S.
    I may be understanding this wrong, but when DNA separates, a new strand forms that is identical to the one it separated from. So, wouldn't those double helices of DNA be identical to each other?
    (2 votes)
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    • purple pi purple style avatar for user emmaw
      When DNA separates to replicate, DNA polymerase (and the other enzymes) attach new bases to each strand, and those new bases are each complementary to the template strand, matching the other original strand that the template strand just broke off from. The end result of this is two completely identical DNA molecules, each having one strand from the original DNA and one strand of new DNA made from surrounding materials, put together by DNA polymerase and other enzymes.
      (3 votes)
  • piceratops tree style avatar for user Shane.A.Adair
    isnt the leading and lagging strand different because when unzipping the DNA the halfs are pointing in oppisite directions of one another?
    (2 votes)
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  • blobby green style avatar for user pooniaswati2
    Explain the exonuclease activity of polymerase 1 in eukaryotes...
    (2 votes)
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  • aqualine sapling style avatar for user Yuliannis
    q te dije
    (2 votes)
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