DNA REPLICATION:
Before the lagging-strand DNA exits the replication factory, its RNA primers must be removed and the Okazaki fragments must be joined together to create a continuous DNA strand. The first step is the removal of the RNA primer. RNAse H, which recognizes RNA-DNA hybrid helices, degrades the RNA by hydrolyzing its phosphodiester bonds. Next, the sequence gap created by RNAse H is then filled in by DNA polymerase which extends the 3' end of the neighboring Okazaki fragment. Finally, the Okazaki fragments are joined together by DNA ligase that hooks together the 3' end of one fragment to the 5' phosphate group of the neighboring fragment in an ATP- or NAD+-dependent reaction.
REPLICATION IN ACTION
We are now ready to review the steps of DNA replication.
The process begins when the helicase enzyme unwinds the double helix to expose two single DNA strands and create two replication forks. DNA replication takes place simultaneously at each fork. The mechanism of replication is identical at each fork. Remember that the proteins involved in replication are clustered together and anchored in the cell. Thus, the replication proteins do not travel down the length of the DNA. Instead, the DNA helix is fed through a stationary replication factory like film is fed through a projector.
Single-strand binding proteins, or SSBs, coat the single DNA strands to prevent them from snapping back together. SSBs are easily displaced by DNA polymerase.
The primase enzyme uses the original DNA sequence as a template to synthesize a short RNA primer. Primers are necessary because DNA polymerase can only extend a nucleotide chain, not start one.
DNA polymerase begins to synthesize a new DNA strand by extending an RNA primer in the 5' to 3' direction. Each parental DNA strand is copied by one DNA polymerase. Remember, both template strands move through the replication factory in the same direction, and DNA polymerase can only synthesize DNA from the 5' end to the 3' end. Due to these two factors, one of the DNA strands must be made discontinuously in short pieces which are later joined together.
As replication proceeds, RNAse H recognizes RNA primers bound to the DNA template and removes the primers by hydrolyzing the RNA.
DNA polymerase can then fill in the gap left by RNase H.
The DNA replication process is completed when the ligase enzyme joins the short DNA pieces together into one continuous strand.
| 6257430954 | DNA Replication | the process of making identical copies of DNA before cell division |  | 0 |
| 6257430955 | Origin of Replication | Specific sequence of DNA where DNA synthesis begins. |  | 1 |
| 6257430956 | replication fork | A Y-shaped region on a replicating DNA molecule where new strands are growing. (The replication fork is half of the replication bubble.) |  | 2 |
| 6257430957 | Semiconservative replication | Each half of an original DNA molecule serves as a templete for a new strand, and the two new DNA molecules each have one old and one new strand. |  | 3 |
| 6257430958 | helicase | An enzyme that unwinds the double helix of DNA and separates the DNA strands in preparation for DNA replication. |  | 4 |
| 6257430959 | DNA Polymerase III | Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule. Main enzymes that copies the template strand into the new strand in prokaryotes. | | 5 |
| 6257430960 | RNA Primer | Sequence of RNA nucleotides bound to a region of single-stranded DNA to initiate DNA replication. |  | 6 |
| 6257430961 | leading strand | the strand of DNA that is continuously synthesized during replication | | 7 |
| 6257430962 | lagging strand | The strand that is synthesized in fragments using individual sections called Okazaki fragments | | 8 |
| 6257430963 | Okazaki fragments | Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand. |  | 9 |
| 6257430964 | DNA ligase | enzyme which connects the individual okazaki fragments on the lagging strand by forming covalent bonds | | 10 |
| 6257430965 | direction of replication | [5 to 3 direction]; In DNA synthesis, new nucleotides are joined one at a time to the 3' end of the newly synthesized strand. DNA polymerases, the enzymes that synthesize DNA, can add nucleotides only to the 3' end of the growing strand and so new DNA strands always elongate in the same 5' to 3' direction. As the DNA unwinds, the template strand that is exposed in the 3' to 5' direction allows the new strand to be synthesized continuously in the 5' to 3' direction. The new strand that undergoes continuous replication is the leading strand. The other template is in the 5' to 3' direction. So the new strand goes 3' to 5' but the replication runs out of template since synthesis is from 5' to 3' always, then more has unwound and it starts again. The newly made strand undergoes discontinuous replication is the lagging strand. Each short length is the Okazaki fragments. | 11 | |
| 6257430966 | topoisomerase | A protein that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork. | | 12 |
| 6257430967 | single-strand binding proteins (SSBs) | Holds the separate strands apart so they are unable to pull back together. Allows template strand to be copied. | 13 | |
| 6257430968 | Nuclease | A DNA cutting enzyme that excises (removes) DNA, especially damaged DNA. |  | 14 |
| 6257430969 | double helix | The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape. |  | 15 |
| 6257430970 | RNA primase | An enzyme that creates a short RNA primer for initiation of DNA replication. | | 16 |
| 6257430971 | adenine | A nitrogen base found in DNA and RNA. It pairs with thymine in DNA and with uracil in RNA |  | 17 |
| 6257430972 | guanine | A nitrogen base found in both DNA and RNA; pairs only with cytosine. |  | 18 |
| 6257430973 | thymine | A nucleotide that pairs with adenine. Found only in DNA. | | 19 |
| 6257430974 | cytosine | A nitrogenous base found in DNA and RNA; pairs with guanine | | 20 |
| 6257430975 | hydrogen bond | A weak chemical bond formed when the slightly positive hydrogen atom of a polar molecule is attracted to the slightly negative atom of another polar molecule. It holds the DNA molecules together. |  | 21 |
| 6257430976 | complimentary | Refers to the base-pairing rules where A matches T and C matches G. (Apple in the tree. Car in the garage.) |  | 22 |
| 6257430977 | base pairs | Any of the pairs formed between complimentary bases in the two nucleotide chains of DNA, such as A-T and C-G (DNA); A-U and C-G (RNA). |  | 23 |
| 6257430978 | mutation | A change in the order of the bases in an organism's DNA; by deletion, insertion, or substitution. |  | 24 |
| 6257430979 | trait | A characteristic that an organism can pass on to its offspring through its genes. |  | 25 |
| 6257430985 | Rosalind Franklin | British scientist who took excellent x-Ray diffraction pictures that provided evidence of double helix. |  | 26 |
| 6257430988 | Chargaff | Analyzed DNA from many species. Found that [A=T] and [G=C] aka [pyrimidines=purines]. Found that ratio of (A+T)/(G+C) varied within organisms but same within a species |  | 27 |
| 6257430989 | antiparallel | Format of two strands in DNA (one 3' to 5', other 5' to 3') |  | 28 |
| 6257430990 | DNA polymerase I | Essential for removing the RNA primers from the fragments and replacing it with the required nucleotides | | 29 |
