Describe the 3-D structure of DNA, making use of the following terms or phrases: sugar-phosphate backbones, 5’ phosphate, 3’ hydroxyl, complementary base-pairing, antiparallel strands, and the number of base pairs ‘per turn’ of the helix.
- DNA is a double helical structure. Each spiral strand composed of a sugar-phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding between paired bases, adenine with thymine and guanine with cytosine.
- The strands run antiparallel to each other, meaning that their subunits run in opposite directions. The deoxyribose sugars are joined at both the 5’ phosphate groups and the 3’ hydroxyl groups. Each turn of the helix contains 10 layers of bases.
Is there any relationship between adjacent nucleotides in a single DNA chain? How about nucleotides positioned across from one another in double-stranded DNA? And finally adjacent base pairs in double-stranded DNA?
• Aside from the bonding between the deoxyribose and phosphate group along the backbone of the strand, there is no relationship between the nucleotides next to one another. As for nucleotides positioned across from one another in a double-stranded DNA, purines always are paired with pyrimidines. There is no relationship in adjacent base pairs in a double-stranded DNA.
Explain the semiconservative model of DNA replication.
The semiconservative model of DNA shows how each new DNA contains one old (parental) and one new strand (daughter).
What is the fate of the original DNA chains when new DNA is made?
The original DNA strands functions as a template for synthesis of a new, complementary strand.
Where does DNA synthesis begin on a chromosome?
DNA synthesis begins at the origins of replication, where the two DNA strands are separated, opening up a replication “bubble”. Replication proceeds in both directions from each origin, until the entire molecule is copied.
How many ‘starting places’ does a bacterial chromosome have? A eukaryotic chromosome?
A bacterial chromosome has one circular origin while eukaryotic chromosome has hundreds to thousands of replication origins.
Explain the basics of replication.
- First, helicase unwinds DNA. Then molecules (single strand binding proteins) bind to unwound DNA and stabilize it. DNA polymerase synthesizes leading strand always adding to the 3’ end of a preexisting chain.
- Then primase begins synthesis of RNA primer for the fifth Okazaki fragments of the lagging strand. The DNA polymerase is completing synthesis of the fourth fragment when it reaches the RNA primer of the third fragment. It will detach and begin adding DNA nucleotides to the 3’ end of the fifth fragment primer in the replication fork.
- DNA polymerase removes the primer from the 5’ end of the second fragment and replaces it with DNA nucleotides that it adds one by one to the 3’ end of the third fragment. The replacement of the last RNA nucleotide with DNA leaves sugar phosphate backbone with a free 3’ end.
- Lastly, DNA ligase joins the 3’ end of the second fragment to the 5’ end of the first fragment.
What enzyme catalyzes DNA synthesis? In what direction does it read a template strand? In what direction does it build a new strand?
DNA polymerase catalyzes DNA synthesis.
It reads a template strand in the 3’ to 5’ direction.
A new strand is built from the 3’ end onwards
Why does DNA synthesis require a primer?
DNA synthesis requires a primer because a DNA cannot initiate a new strand. Another enzyme must make another polynucleotide for DNA polymerase to add on
What is a primer, what is it made of, what makes it, and how?
A primer is an RNA chain synthesized by a primase starting a complementary RNA chain from a single RNA nucleotide, adding RNA nucleotides one at a time using the parental DNA strand as a template. Primer is 5-10 nucleotides long and is based paired to the template strand. A new DNA strand will start from the 3’ end of RNA primer.
Explain the details of DNA replication, making use of the following terms or phrases: template strands, helicase, single strand binding protein, primase, and complementary base pairing.
- First, helicase is needed to unwind the coiled double-helix structure, so that the individual strands of DNA can be exposed.
- Then, single strand binding proteins bind to the individual strands and prevent them from wrapping back around one another.
- The enzyme primase creates an RNA primer which serves as a starting point for DNA polymerase to begin synthesis of new DNA.
- On the leading strand, the process proceeds in a straight-forward manner once the primer has been placed. The leading stand synthesis is said to be continuous in the 5’ to 3’ direction. In lagging strand synthesis, a primer is still needed from primase just like the leading strand.
- Once the primer has been placed, the DNA polymerase can extend the lagging strand. RNA primer always lies behind it. Ligase comes in last to join the Okazaki fragments together.
Explain how the primers used for lagging strand synthesis are removed and replaced with DNA.
Primers used for lagging strand synthesis are removed and replaced when DNA polymerase I reaches the primers to replace it with DNA.
role of Okazaki fragments and DNA ligase
Okazaki fragments are a series of segments on a lagging strand. DNA ligase is an enzyme which joins sugar-phosphate backbones of all Okazaki fragments into continuous DNA stands.
What are histone proteins?
Histone is small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in chromatin structure.
Know the various enzymes, such as polymerase and nuclease, discussed in this chapter.
Nuclease, Telomerase, DNA polymerase, Primase, Helicase, Topoisomerase, DNA ligase, and RNA polymerase
Nuclease
an enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.
Telomerase
catalyzes the lengthening of telomeres in germ cells
DNA polymerase
catalyze the elongation of new DNA at a replication fork.
Primase
adds RNA nucleotides one at a time using the parental DNA as a template.
Helicase
are enzymes that untwist the double helix at the replication forks.
Topoisimerase
corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands.
DNA Ligase
links together the sugar—phosphate backbones of all the individual Okazaki fragments into a continuous strand.
RNA polyerase
links ribonucleotides into a growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand.
In what molecules other than DNA is adenine found?
- Multiple adenine nucleotides are found at the 3’ end of an mRNA, forming a poly-A tail.
- It is also found on transfer RNA.
