DNA Structure and Replication Flashcards
What are nucleic acids
Nucleic acids are macromolecules that exist as polymers called polynucleotides. Each polynucleotide is composed of repeating units/monomers called nucleotides.
What is the key difference between ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)?
The pentose sugar in RNA is ribose, and ribose-containing nucleotides, ribonucleotides are the monomers of RNA. The pentose sugar in DNA is deoxyribose, deoxyribose-containing nucleotides, deoxynucleotides, are the monomers of DNA.
What is the main difference between ribose and deoxyribose sugars?
At the 2’ carbon of deoxyribose, the hydroxyl group (-OH) is replaced by a hydrogen
atom (H).
This small difference has led to significant differences in structure and therefore, functions of the two types of nucleic acids. The partial negative charge of the hydroxyl group in ribose repels the negative charge of the phosphate, preventing the chain from coiling in as tight a helix as it does in DNA.
Hence, RNA is more susceptible to chemical and enzyme degradation
Why is RNA more susceptible to chemical and enzyme degradation than DNA?
At the 2’ carbon of deoxyribose, the hydroxyl group (-OH) is replaced by a hydrogen
atom (H).
This small difference has led to significant differences in structure and therefore, functions of the two types of nucleic acids. The partial negative charge of the hydroxyl group in ribose repels the negative charge of the phosphate, preventing the chain from coiling in as tight a helix as it does in DNA.
Hence, RNA is more susceptible to chemical and enzyme degradation
Describe what is a nitrogenous base and name the types with the differences
A nitrogenous base has a nitrogen-containing ring structure.
The nitrogenous bases fall into two types: purines and pyrimidines. Purines have a 6-membered ring fused to a 5-membered ring; pyrimidines have a 6-membered ring
Name the types of base each nucleic acid has [AT(U)GC]
DNA: Purine bases - Adenine - Guanine Pyrimidine bases - Cytosine - Thymine
RNA Purine bases - Adenine - Guanine Pyrimidine bases - Cytosine - Uracil
What is a nucleoside
The combination of a pentose with a nitrogenous base forms a compound called a nucleoside This occurs with the elimination of water and therefore is a condensation reaction. 1’ carbon of the pentose is linked in a glycosidic bond to the nitrogenous base.
How is a nucleotide formed
A nucleotide is formed by further condensation between the nucleoside and phosphate group, forming a phosphoester bond between the 5’ carbon of pentose and the phosphate group.
Describe the formation of dinucleotides and polynucleotides
Two nucleotides join to form a dinucleotide by condensation between the 5’·phosphate group of one nucleotide and the 3’-hydroxyl group of the other to form a phosphodiester bond.
The condensation reaction between nucleotides is repeated several millions times to form a polynucleotide i.e. DNA or RNA
Phosphodiester bonds between 5’ phosphate and 3’ hydroxyl groups of nucleotides form a linear, unbranched sugar-phosphate backbone.
Phosphodiester bonds are strong covalent bonds. They confer strength and stability on the polynucleotide chain. This is the basis in preventing breakage of the chain during DNA replication.
Describe what is the polarity/directionality of a polynucleotide.
The manner in which deoxyribonucleoside triphosphates are added to the 3’ end of a growing chain has resulted in a polynucleotide molecule that has polarity or directionality. Each DNA or RNA strand I chain has two free ends that are chemically different from each other
5’ end with a free 5’ carbon carrying a phosphate group; and
3’ end with a free 3’ carbon carrying a hydroxyl (-OH) group
Thus, every DNA or RNA molecule has an intrinsic polarity or directionality. The DNA or RNA base sequence is read in a 5’ to 3’ direction.
What is Chargaff’s rule and what were its consequences?
Amount of A=T, and amount of G=C
This resulted in the development of the double-helix DNA model involving specific complementary base-pairing between A on one DNA strand and T on the other, and between G on one strand and C on the other.
Thus, the specific sequence of bases on one DNA strand determines the specific order of bases on the other complementary strand.
Name the observations that led to Chargaff’s rules
The base composition of the DNA of an organism is constant throughout all the somatic cells of that organism and is characteristic for a given species.
(Somatic cells include all body cells other than the gametes.)
There is always equal proportion of adenine (A) and thymine (T) and equal proportion of guanine (G) and cytosine (C)
There is always an equal proportion of purines (A+ G) and pyrimidines (C + T)
Describe the main features of the DNA double helix proposed by Watson and Crick
DNA consists of two polynucleotide strands/chains. Each strand forms a right-handed helix and the two strands coil around each other to form a double-helix.
The diameter of the helix is uniformly 2 nm. Hence, there is just enough space for 1 purine and 1 pyrimidine in the centre of the double-helix.
The strands run in opposite directions, i.e. they are antiparallel. One strand is oriented in the 5’ to 3’ direction whilst the other is oriented in the 5’ direction.
Each strand has a sugar-phosphate backbone with:
a. phosphate groups that project outside the double-helix since they are hydrophilic; and
b. nitrogenous bases that orientate inwards toward the central axis at almost right angles.
This arrangement is appealing because it puts the relatively hydrophobic nitrogenous bases in the molecules interior and thus away from the surrounding aqueous medium.
The bases of the opposite strands are bonded together by relatively weak hydrogen bonds
Terminology: 1 DNA molecule = 1 DNA double-helix = 2 polynucleotide strands/chains
Describe the characteristics of the phosphate groups and nitrogenous bases that determine the double helix structure
Phosphate groups project outside the double-helix since they are hydrophilic.
Nitrogenous bases that orientate inwards toward the central axis at almost right angles, due to their hydrophobicity.
This arrangement is appealing because it puts the relatively hydrophobic nitrogenous bases in the molecules interior and thus away from the surrounding aqueous medium.
State the pairing between the nitrogenous bases in DNA
Specific, complementary base-pairing occurs between A and T (2 hydrogen bonds) and between C and G (3 hydrogen bonds)
