Chapter 8 Flashcards
(32 cards)
What is the structure of a nucleotide? Nucleoside?
A nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group. A nucleoside consists of a nitrogenous base and pentose - does NOT include the phosphate group.
Each component contributes to the overall structure and function of nucleotides in nucleic acids.
What are the two types of nitrogenous bases?
Pyrimidines and purines
Pyrimidines include cytosine, thymine, and uracil, while purines include adenine and guanine.
What are the five major nitrogenous bases?
Adenine, guanine, cytosine, thymine, uracil
These bases are crucial for the structure of DNA and RNA.
How is each nitrogenous base attached to the nucleotide?
By a glycosidic bond (N-beta-glycosyl at 1’ carbon)
This bond connects the base to the sugar component of the nucleotide.
What is the charge of a nucleotide at neutral pH?
Negative
The phosphate group contributes to the overall negative charge. As a result the backbone is very hydrophilic
What is the structure of pentose sugar in nucleotides?
A five-carbon sugar (ribofuranose)
In DNA, it is deoxyribose, and in RNA, it is ribose. The pentose is not planar
What is the difference between DNA and RNA?
DNA contains beta-2’-deoxy-D-ribofuranose and thymine; RNA contains beta-D-ribofuranose and uracil
This difference affects their structure and function.
Where is the phosphate group attached to the nucleotide?
To the 5’ carbon of the pentose sugar
The phosphate group can also vary in number, allowing for different nucleotide types (ex. ATP). The phosphate group can also vary in position based on specific function
How many phosphates can a nucleotide contain?
One or more
Some nucleotides, like ATP, contain three phosphate groups.
What is the backbone of nucleic acids made of?
Alternating sugar and phosphate groups
The backbone provides structural support for the nucleic acid chain.
What is the charge of the nucleic acid backbone at neutral pH?
Negative
This is due to the phosphate groups in the backbone. Creates a very hydrophilic environment
What are the properties of nitrogenous bases?
Planar, hydrophobic, and capable of forming hydrogen bonds
These properties facilitate base pairing and stacking interactions.
What type of noncovalent interaction exists between complementary bases?
Hydrogen bonds
These bonds stabilize the double helix structure of DNA.
How do the bases pair in DNA?
A pairs with T and C pairs with G
This complementary pairing is critical for accurate DNA replication.
What stabilizes the double helix structure of DNA?
Hydrophobic interactions and base stacking interactions (pi-pi stacking, van der waals, dipole-dipole)
These forces maintain the integrity of the DNA structure.
How many base pairs are there per turn in the DNA double helix?
Approximately 10 base pairs.
This number can vary slightly depending on the DNA sequence and conditions. In solution, it is about 10.5 base pairs per helical turn (one turn is 36 angstroms)
What is a DNA palindrome?
A sequence of DNA that reads the same forward and backward
Palindromic sequences are often involved in the binding of proteins.
What is triplex DNA?
A structure formed by three strands of DNA. Usually the third base pair joins in the major groove. Creates Hoogsteen pairs.
Most stable at low pH. Forms most readily when only purines or pyrimidines are in a strand.
How are guanine and adenine differentiated?
Adenine contains a amine group off carbon 6.
Guanine contains a carbonyl on carbon 6, and an amine group on carbon 2.
How are uracil, thymine and cytosine differentiated?
Uracil has a carbonyl group on carbons 2 and 4.
Thymine has a methyl group on carbon 5 and a carbonyl on carbons 2 and 4.
Cytosine has an amine group on carbon 4 and a carbonyl group on carbon 2.
Which is more hydrophilic? Nucleic backbone or the nitrogenous bases?
Nucleic backbone due to the phosphate groups
How many hydrogen bonds are between pairs?
Adenine forms 2 hydrogen bonds between thymine or uracil.
Guanine forms 3 hydrogen bonds with cytosine.
What is B form double helical DNA?
The Watson-Crick model. Two strands are antiparallel and complementary. Backbone faces out. Nitrogenous bases on inside with rings planar, stacked on top of each other, perpendicular to axis. Major and minor grooves due to offset strands. Base pairs are 3. 4 angstroms apart, with 10 base pairs per turn.
What force provides complementarity?
Hydrogen bonding. Does not have great impact stability.
