DNA: Subunits & Structure Flashcards
What are the three chemical constituents of DNA?
- Deoxyribose sugar
- A phosphate group
- Four nitrogenous bases
What are the two subtypes of nitrogenous bases, and how are they different?
The two types are purines and pyrimidines. Purines have a pyrimidine ring fused to an imidazole ring while pyrimidines have a pyrimidine hetero cyclic ring. They can also be distinguished based on the group attached to the 1’ carbon. For purines, N9, and for pyrimidines, N1.
What is the difference between ribose (on RNA) and deoxyribose (DNA) sugars?
The key difference is on the 2’C. On ribose, this carbon has a hydroxyl group (OH). On deoxyribose, it has H.
On the 5-carbon ribose sugar of a nucleotide, where is the nitrogenous base located?
The 1’ carbon.
On the 5-carbon ribose sugar of a nucleotide, where is the phosphate group located?
The 5’ carbon.
What differentiates nucleosides from nucleotides?
Nucleosides are different from nucleotides because of the presence or absence of a phosphate group.
How are nucleotide analogs used in anti-cancer and anti-viral drugs?
Analogs are close structural relatives of nucleotides and can be used in drugs by substituting for the normal nucleotide. This causes the chain synthesis to terminate because there is an “incorrect” base or sugar being added. An example is the nucleoside analogue Remdesivir, which is an adenosine analogue that interferes with RNA replication in the Covid-19 virus.
Where does the formation of a phosphodiester bond occur in the assembly of nucleic acid strands?
The phosphodiester bonds form between the 5’ phosphate of one nucleotide and the 3’ hydroxyl of another nucleotide.
What does G bind to in the DNA duplex, and how many hydrogen bonds does it form?
G binds to C with three hydrogen bonds.
What does A bind to in the DNA duplex, and how many hydrogen bonds does it form?
A binds to T with two hydrogen bonds.
What is the backbone of DNA formed from?
Sugars and phosphate groups.
Compare and contrast the alternative structures for DNA.
A-form: Only found in dehydrated samples in X-ray crystals; forms a right-handed duplex.
Z-form: Thought to exist as a transient structure to reduce supercoiling strain during transcription; forms a left-handed duplex.
Triple helix: Has 3rd strand H-bonded to B-DNA duplex via unusual Hoogsteen bonds and involved in the regulation of gene expression; forms a right-handed duplex.
Describe the effects of supercoiling on circular DNA in electrophoresis gels and the impact of under- and over-winding.
Supercoiled DNA migrates faster in electrophoresis gels than relaxed circular DNA because of its tight winding DNA is underwound if it has >10 base pairs/turn, which leads to negative supercoiling (fewer turns/overall length. DNA is overwound if it has <10 base pairs/turn, which leads to positive supercoiling (more turns/overall length).
Describe the catalytic properties of RNA.
RNA can form ribozymes and is responsible for forming the peptide bonds critical for protein translation. RNA single strands are also capable of forming complex structures by folding back upon themselves.
Describe the RNA world hypothesis.
The RNA world hypothesis says that life based on ribonucleic acid (RNA) predates the current world of life based on DNA, RNA, and proteins. This is possible because RNA is able to store genetic information like DNA and catalyze chemical reactions like an enzyme protein.
How do the size of eukaryotic chromosomes/genomes compare to prokaryotic chromosomes/genomes?
Those of eukaryotes are much larger.
Describe the core molecule around which DNA is wrapped.
DNA is wound 1.8x in a left-handed coil around a histone octamer. Histones are proteins that make up the nucleosome. 2 copies of each type of histone for a total of 8 histones make up the histone octamer. This forms the core molecule around which DNA is wrapped.
What is the role of histone H1?
Histone H1 is a linker protein that associates with DNA at an entry and exit site from the nucleosome in two alternate positions.
Describe some important characteristics of histones.
- Histones are rich in basic amino acids (lys/arg) with positive charge.
- Histones are very conserved proteins, meaning there has been little evolutionary change in their structure or function.
- They are small basic proteins that neutralize the negative charge on the phosphate backbone of DNA (which is an extremely negatively charged molecule).
Compare and contrast the two types of chromatin.
Euchromatin and heterochromatin. Euchromatin has diffuse electron density and is involved in active transcription. Heterochromatin has compacted, high electron density and is silent in terms of gene expression.
What is epigenetics, and how does it work?
Epigenetics is essentially chromatin remodeling. Histone modifications influence gene expression: high levels of histone H1 leads to no gene transcription. Reduced levels of histone H1 means gene transcription is possible. This leads to the opening up of the chromatin structure to allow access for the transcription machinery to do its job.
Define nucleic acids.
Nucleic acids are macromolecules constructed out of long chains (strands) of monomers called nucleotides.
What is the function of nucleic acids?
Nucleic acids function primarily in the storage and transmission of genetic information, but they also have structural or catalytic roles.
What are the three parts that compose a nucleotide?
- A five-carbon sugar, ribose.
- A nitrogenous base (so called because nitrogen atoms form part of the rings of the molecule).
- A phosphate group.
Which two parts of the nucleotide make up a nucleoside?
The sugar and nitrogenous base.
Which carbon of the ribose sugar is the phosphate linked to?
The 5’ carbon.
Which carbon of the ribose sugar is the nitrogenous base linked to?
The 1’ carbon.
How are nucleotides attached during the assembly of a nucleic acid strand?
The hydroxyl group attached to the 3’ carbon of the sugar of one nucleotide becomes linked by an ester bond to the phosphate group attached to the 5’ carbon of the next nucleotide in the chain. Thus, the nucleotides of a DNA strand are connected by sugar-phosphte linkages called 3’-5’ phosphodiester bonds.
What is the difference between the 5’ and 3’ end of a nucleotide?
A nucleotide has a polarized structure. The end where the phosphate is located is the 5’ end and the other end is the 3’ end.
What is the relationship between the number of purines in a given sample of DNA and the number of pyrimidines?
The number of purines is always equal to the number of pyrimidines.
Define chromatin.
Chromatin is a composition of DNA and its associated proteins that together form chromosomes.
What are histones?
Histones are a group of small proteins that possess an unusually high content of the basic amino acids arginine and lysine, and they are responsible for the orderly packaging of eukaryotic DNA.
What are nucleosomes?
Nucleosomes are repeating subunits that organize DNA and histones.
Describe the structure of a nucleosome.
Each nucleosome contains a nucleosome core particle consisting of 146 base pairs of supercoiled DNA wrapped almost twice around a disk-shaped complex of eight histone molecules.
Describe the structure of the histone core of a nucleosome.
The histone core consists of two copies each of histones H2A, H2B, H3, and H4 assembled into an octamer. The eight histone molecules are organized into four heterodimers: two H2A-H2B dimers and two H3-H4 dimers. The remaining histone–H1–resides outside the nucleosome core particle.
Describe the levels of organization of chromatin.
Naked DNA molecules are wrapped around histones to form nucleosomes, which represent the lowest level of chromatin organization. Nucleosomes are organized into 30-nm fibers, which in turn are organized into looped domains. When cells prepare for mitosis, the loops become further compacted into mitotic chromosomes.
