The phosphoanhydride bonds between that link the phosphate groups to each other have specific chemical properties that make them good for various biological functions. The hydrolysis of the bonds between the phosphate groups is thermodynamically exergonic in biological conditions; nature has evolved numerous mechanisms to couple this negative change in free energy to help drive many reactions in the cell. Figure 2 shows the structure of the nucleotide triphosphate Adenosine Triphosphate, ATP, that we will discuss in greater detail in other chapters.
The term "high-energy bond" is used A LOT in biology. This term is, however, a verbal shortcuts that can cause some confusion. The term refers to the amount of negative free energy associated with the hydrolysis of the bond in question. The water or other equivalent reaction partner is an important contributor to the energy calculus. In ATP, for instance, simply "breaking" a phosphoanhydride bond - say with imaginary molecular tweezers - by pulling off a phosphate would not be energetically favorable.
We must, therefore, be careful not to say that breaking bonds in ATP is energetically favorable or that it "releases energy". Rather, we should be more specific, noting that they hydrolysis of the bond is energetically favorable. Some of this common misconception is tied to, in our opinion, the use of the term "high energy bonds". While in Bis2a we have tried to minimize the use of the vernacular "high energy" when referring to bonds, trying instead to describe biochemical reactions by using more specific terms, as students of biology you will no doubt encounter the potentially misleading - though admittedly useful - short cut "high energy bond" as you continue in your studies.
So, keep the above in mind when you are reading or listening to various discussions in biology. Heck, use the term yourself. Just make sure that you really understand what it refers to. DNA has a double helix structure shown below created by two strands of covalently linked nucleotide subunits. The sugar and phosphate groups of each strand of nucleotides are positioned on the outside of the helix, forming the backbone of the DNA highlighted by the orange ribbons in Figure 3.
We referred to this orientation of the two strands as antiparallel. Note too that phosphate groups are depicted in Figure 3 as orange and red "sticks" protruding from the ribbon. The phosphates are negatively charged at physiological pHs and therefore give the backbone of the DNA a strong local negatively charged character.
By contrast, the nitrogenous bases are stacked in the interior of the helix these are depicted as green, blue, red, and white sticks in Figure 3. Pairs of nucleotides interact with one another through specific hydrogen bonds shown in Figure 5. Each pair of separated from the next base pair in the ladder by 0. The specific chemistry associated with these interactions is beyond the content of Bis2a but is described in more detail here for the curious or more advanced students.
We do expect, however, that students are aware that the stacking of the nitrogenous bases contributes to the stability of the double helix and defer to your upper-division genetics and organic chemistry instructors to fill in the chemical details. Figure 3. Use the BACK button on your browser to return here later.
Note: You might have noticed that I have shorten the chains by one base pair compared with the previous diagram. There isn't any sophisticated reason for this. The diagram just got a little bit too big for my normal page width, and it was a lot easier to just chop a bit off the bottom than rework all my previous diagrams to make them slightly smaller!
This diagram only represents a tiny bit of a DNA molecule anyway. Notice that the two chains run in opposite directions, and the right-hand chain is essentially upside-down.
You will also notice that I have labelled the ends of these bits of chain with 3' and 5'. If you followed the left-hand chain to its very end at the top, you would have a phosphate group attached to the 5' carbon in the deoxyribose ring. If you followed it all the way to the other end, you would have an -OH group attached to the 3' carbon.
This 5' and 3' notation becomes important when we start talking about the genetic code and genes. The genetic code in genes is always written in the 5' to 3' direction along a chain. It is also important when we take a very simplified look at how DNA makes copies of itself on the next page.
If this is the first set of questions you have done, please read the introductory page before you start. To the amino acid and other biochemistry menu. A quick look at the whole structure of DNA These days, most people know about DNA as a complex molecule which carries the genetic code.
You read 3' or 5' as "3-prime" or "5-prime". Attaching a phosphate group The other repeating part of the DNA backbone is a phosphate group. Attaching a base and making a nucleotide The final piece that we need to add to this structure before we can build a DNA strand is one of four complicated organic bases. These bases attach in place of the -OH group on the 1' carbon atom in the sugar ring. What we have produced is known as a nucleotide. Here are their structures: The nitrogen and hydrogen atoms shown in blue on each molecule show where these molecules join on to the deoxyribose.
For example, here is what the nucleotide containing cytosine would look like:. Now we can simplify all this down to the bare essentials! We can build the chain based on this fairly obvious simplification: There is only one possible point of confusion here - and that relates to how the phosphate group, P , is attached to the sugar ring. Joining the two DNA chains together The importance of "base pairs" Have another look at the diagram we started from: If you look at this carefully, you will see that an adenine on one chain is always paired with a thymine on the second chain.
So how exactly does this work? But, more than this, the pairing has to be exactly. The base pairs fit together as follows. A final structure for DNA showing the important bits. The DNA double helix looks like a twisted staircase, with the sugar and phosphate backbone surrounding complementary nitrogen bases. DNA has a double-helix structure, with sugar and phosphate on the outside of the helix, forming the sugar-phosphate backbone of the DNA. The nitrogenous bases are stacked in the interior in pairs, like the steps of a staircase; the pairs are bound to each other by hydrogen bonds.
The two strands of the helix run in opposite directions. This antiparallel orientation is important to DNA replication and in many nucleic acid interactions. The phosphate backbone indicated by the curvy lines is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand.
Only certain types of base pairing are allowed. This means Adenine pairs with Thymine, and Guanine pairs with Cytosine. This is known as the base complementary rule because the DNA strands are complementary to each other. Antiparallel Strands : In a double stranded DNA molecule, the two strands run antiparallel to one another so one is upside down compared to the other. The phosphate backbone is located on the outside, and the bases are in the middle.
Adenine forms hydrogen bonds or base pairs with thymine, and guanine base pairs with cytosine. At this time it is possible a mutation may occur. A mutation is a change in the sequence of the nitrogen bases. Most of the time when this happens the DNA is able to fix itself and return the original base to the sequence. However, sometimes the repair is unsuccessful, resulting in different proteins being created.
DNA packaging is an important process in living cells. Without it, a cell is not able to accommodate the large amount of DNA that is stored inside.
A eukaryote contains a well-defined nucleus, whereas in prokaryotes the chromosome lies in the cytoplasm in an area called the nucleoid. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together? Eukaryotic and prokaryotic cells : A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.
Base-pairing takes place between a purine and pyrimidine: namely, A pairs with T, and G pairs with C. In other words, adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. Adenine and thymine are connected by two hydrogen bonds, and cytosine and guanine are connected by three hydrogen bonds. The diameter of the DNA double helix is uniform throughout because a purine two rings always pairs with a pyrimidine one ring and their combined lengths are always equal.
Figure 9. There is a second nucleic acid in all cells called ribonucleic acid, or RNA. Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group.
In the case of RNA, the five-carbon sugar is ribose, not deoxyribose. RNA nucleotides contain the nitrogenous bases adenine, cytosine, and guanine. Molecular biologists have named several kinds of RNA on the basis of their function.
For this reason, the DNA is protected and packaged in very specific ways. In addition, DNA molecules can be very long. Stretched end-to-end, the DNA molecules in a single human cell would come to a length of about 2 meters.
Thus, the DNA for a cell must be packaged in a very ordered way to fit and function within a structure the cell that is not visible to the naked eye. The chromosomes of prokaryotes are much simpler than those of eukaryotes in many of their features Figure 9. Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm called the nucleoid.
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