MODULE 2: Chapter 3.1 Flashcards
What are the building blocks of DNA and RNA?
Nucleotides
Nucleotides are linked together through a phosphodiester backbone into a linear chain.
What three components make up a nucleotide?
Nitrogenous base, ribose or deoxyribose sugar, phosphate groups.
What is the difference between a nucleoside and a nucleotide?
Nucleoside consists of a base and a sugar; nucleotide is a phosphorylated nucleoside.
What are the two types of nitrogenous bases found in DNA and RNA?
Purines and pyrimidines.
What is the furanose ring in nucleosides characterized by?
It is ‘puckered’ and exists in C-2′ endo and C-3′ endo conformations.
What suffix is used for the generic names of nucleoside monophosphates?
-ylate.
How are deoxyribonucleotides abbreviated?
With a ‘d’ at the beginning of the abbreviation.
What is the primary structure of DNA and RNA?
The unique arrangement of deoxyribonucleotides or ribonucleotides in a single chain.
What is the secondary structure of DNA?
Two complementary strands of DNA bind together through base pairing in an antiparallel fashion.
What is the well-known secondary structure of DNA?
The double helix.
What is the approximate size range of prokaryotic chromosomes?
0.6 million to more than 10 million base pairs.
What is Chargaff’s rule?
A = T and C = G.
What type of bonds hold the base pairs together in DNA?
Hydrogen bonds.
How many hydrogen bonds are formed between G-C base pairs?
Three hydrogen bonds.
How many hydrogen bonds are formed between A-T base pairs?
Two hydrogen bonds.
What base pairs with adenine in RNA?
Uracil.
What is the distance between adjacent base pairs in DNA?
3.4 Å.
What is the average number of base pairs per turn in the DNA double helix?
10.5 base pairs.
Fill in the blank: The coding strand of DNA has the same base sequence as the _______.
RNA transcript.
True or False: Prokaryotic DNA is typically linear.
False.
What is the typical diameter of a bacterial cell?
1 µm.
What is the role of the major groove in DNA?
It is often the site where proteins specifically bind to DNA.
What are the two main forms of nitrogenous bases in nucleotides?
Purines and pyrimidines.
What is the role of the sugar-phosphate backbone in DNA?
It is polar and exposed to water, providing structural support.
What is the significance of the puckered conformation of the ribose sugar?
It allows for the formation of nucleosides.
What type of bonds form between adenine and thymine?
Two hydrogen bonds
Hydrogen bonds are shown as dashed red lines between the bases.
What is the term for the arrangement of base pairs in a DNA double helix?
Antiparallel strands
The DNA sequence is conventionally listed in the 5′ to 3′ direction.
What is base stacking in DNA?
Base pairs are stacked upon each other within van der Waals contact distance
This arrangement provides enthalpic stability to the DNA molecule.
Which type of interactions contribute significantly to the stability of the DNA double helix?
Van der Waals forces
These forces are additive and contribute significantly to the stability of the molecule.
What effect does the hydrophobic nature of DNA bases have on stability?
It sequesters the bases from interacting with water
This is entropically favorable.
What is the primary source of stability in a DNA double helix?
Base stacking interactions
Hydrogen bonding contributes less to overall stability.
What is the melting temperature (Tm) of DNA?
The temperature at which half of the DNA molecules are denatured
Tm can be monitored by changes in absorbance at 260 nm.
How does the G-C content affect the Tm of DNA?
As G-C content increases, Tm increases
G-C base pairs have more favorable stacking interactions.
What is the shape difference between A-DNA, B-DNA, and Z-DNA?
A-DNA is short and wide, B-DNA is standard, Z-DNA is narrow
A-DNA allows 11 base pairs per turn, B-DNA allows 10.5, and Z-DNA allows 12.
What type of helical structure is Z-DNA?
Left-handed helical structure
Unlike A-DNA and B-DNA, which are right-handed.
What is the biological significance of Z-DNA?
Not fully understood, but it has been detected in vivo
Proteins that preferentially bind Z-DNA have also been identified.
What is the hyperchromic effect in DNA?
Single-stranded DNA absorbs more UV light than double-stranded DNA
This property can be used to monitor denaturation.
What influences the ease of DNA strand separation?
Base composition and length of the molecule
Solution conditions, including ionic strength, also play a role.
What must occur for DNA replication or transcription to begin?
Strand separation within a specific region of DNA
This allows replication or transcription complexes to bind.
What is the role of helicases in DNA?
Enzymes that separate DNA strands
They unwind the double helix and disrupt hydrogen bonds.
How does the length of the DNA strand affect its stability?
Longer strands have greater stabilizing forces
More heat energy is required to dissociate the strands.
What happens to DNA absorbance as it denatures?
Absorbance increases at 260 nm
This indicates the transition from double-stranded to single-stranded DNA.
True or False: A-T base pairs are more stable than G-C base pairs.
False
G-C base pairs have more favorable stacking interactions.
What factors affect the melting temperature (Tm) of DNA?
The presence of positively charged ions and the length of the DNA strand
Longer strands require more heat energy to dissociate due to greater stabilizing forces.
How does strand length influence Tm?
As the length of the DNA strand increases, the Tm increases
This is illustrated by melting curves showing percent single-stranded DNA plotted against temperature.
What role do Na⁺ ions play in stabilizing DNA?
Na⁺ ions bind to the PO3²⁻ groups in the DNA backbone, neutralizing negative charges and stabilizing the helix
This stabilization raises the Tm.
Define supercoiling in DNA.
Supercoiling is the coiling of DNA upon itself, which allows DNA to fit within the dimensions of a cell nucleus.
What types of supercoiling exist?
Right-handed (negative) supercoiling and left-handed (positive) supercoiling.
What is the linking number (Lk) in circular DNA?
The number of times a strand of DNA winds in the right-handed direction around the helix axis.
What are the two components of the linking number?
Twist (Tw) and writhe (Wr).
What happens to the linking number when one strand of DNA is cut?
The topology of DNA can change, allowing for the addition or removal of turns.
What is the effect of negative supercoiling on DNA processes?
It facilitates DNA replication and transcription by making unwinding and separation easier.
How do topoisomerases relieve supercoiling?
By cleaving and resealing one or both strands of DNA.
Differentiate between type I and type II topoisomerases.
Type I topoisomerases break one strand and reduce supercoiling by one turn; type II topoisomerases break both strands and can reduce or increase supercoiling by two turns.
What is the significance of the ‘RNA world’ hypothesis?
It proposes that life began with RNA, leading to questions about why DNA evolved as the genetic information carrier.
What distinguishes the primary structures of DNA and RNA?
- 2′ carbon in RNA has a hydroxyl group; 2. RNA uses uracil, DNA uses thymine; 3. RNA can form ribozymes.
Fill in the blank: The stability of the DNA helix is increased by the presence of _______.
positively charged ions.
True or False: Supercoiling only occurs in prokaryotic DNA.
False
Supercoiling occurs in both prokaryotic and eukaryotic DNA.
What happens to DNA during transcription regarding supercoiling?
Negative supercoiling occurs upstream, while positive supercoiling occurs downstream of the transcription bubble.
What are the three primary structural differences between DNA and RNA?
- 2′-carbon of ribose in RNA has a hydroxyl group, while DNA does not
- RNA uses uracil, DNA uses thymine
- RNA can form ribozymes; DNA cannot
How does the presence of a 2′-hydroxyl group in RNA affect its stability?
It facilitates spontaneous degradation through autocleavage of the phosphodiester backbone
What is the consequence of RNA’s instability for gene expression?
It allows for quick translation and degradation of mRNA, tightly regulating gene expression
True or False: The instability of RNA makes it suitable for long-term storage of genetic information.
False
What is the role of messenger RNA (mRNA) in relation to protein synthesis?
mRNA must be quickly translated into protein to prevent degradation and regulate gene expression
What happens to cytosine in DNA due to spontaneous deamination?
Cytosine is converted to uracil, leading to potential mutations if not repaired
What is a ribozyme?
An RNA molecule that can catalyze biochemical reactions
What is Ribonuclease P (RNaseP) and its function?
A ribozyme that cleaves nucleic acids, consisting of a 417-nucleotide RNA strand
Fill in the blank: RNA can form complex structures, including _______ and _______.
duplexes; hairpins
What are modified nucleotides in tRNA important for?
They help stabilize the structure and mediate tRNA functions
What is the significance of inosine in tRNA anticodons?
It allows pairing with multiple codons, enabling flexibility in amino acid coding
What are triplet interactions in RNA and DNA?
Complex base pairing interactions involving a single-stranded region binding to a duplex
What are G-quadruplex and I-motif structures?
- G-quadruplex: four guanine bases connected by hydrogen bonds
- I-motif: hydrogen bonds between hemiprotonated cytosine residues
True or False: DNA exists only in the B-form configuration.
False
What role do DNA quadruplex structures play?
They are involved in transcriptional regulation and DNA repair
How does the presence of thymine in DNA help maintain genetic information?
It prevents mutations caused by spontaneous deamination of cytosine
What occurs if uracil is not removed from DNA after cytosine deamination?
It increases the chance of accumulating deleterious mutations
What type of RNA must be stable for longer periods inside the cell?
Transfer RNA (tRNA) and ribosomal RNA (rRNA)
What is the effect of alkaline conditions on RNA?
They facilitate autocleavage by inducing nucleophilic attack on the phosphate backbone
What is the function of enzymes that identify and remove uracil residues in DNA?
To prevent mutations resulting from spontaneous cytosine deamination
What is the I-motif in DNA?
A four-stranded DNA quadruplex structure containing mostly cytosine residues
The I-motif can form hemiprotonated cytosine residues within one strand of DNA.
How many hydrogen bonds form between two cytosine bases in the I-motif?
Three hydrogen bonds
One of the cytosines is protonated on the N-3 atom.
What role do antibodies specific for the I-motif play in the cell cycle?
They bind to many regions in the genome at the G1–S boundary of the cell cycle.
What type of interactions do DNA binding proteins have with nucleotide bases?
Noncovalent interactions
These interactions are sequence-specific or sequence-independent depending on the protein.
What is a nucleosome?
A repeating unit of DNA–histone complexes
Each nucleosome consists of a region of double-stranded helical DNA bound to eight histone proteins.
How many histone proteins are involved in a nucleosome?
Eight histone proteins: two copies each of H2A, H2B, H3, and H4.
What is the function of the linker histone H1?
Connects to the outside of the nucleosome structure and helps keep the ends of the DNA in place.
What mediates histone binding to DNA?
Large, positively charged sections in the protein
These positive charges interact with the negatively charged DNA backbone.
What is the function of single-stranded DNA binding proteins?
To protect single-stranded DNA regions from premature annealing or cleavage by nucleases.
What distinguishes single-stranded DNA from RNA in the binding process?
The binding pocket excludes the 2′-hydroxyl of RNA from binding.
What is the lac repressor protein?
A type of negative regulator that binds a specific region in the bacterial genome to prevent transcription of the lac operon.
How does the lac repressor bind to DNA?
As a homotetramer, meaning four identical copies of the protein bind to an identical DNA sequence.
What is the primary structure of a protein?
The unique arrangement of monomeric subunits in a single polypeptide chain.
What is Chargaff’s rule?
In DNA from any cell of any organism, the percentage of adenine equals the percentage of thymine, and the percentage of guanine equals the percentage of cytosine.
What is denaturation in the context of nucleic acids?
Partial or complete unfolding of the conformation of a nucleic acid chain.
What does the hyperchromic effect refer to?
The increase in light absorbance at 260 nm as double-stranded DNA unwinds and separates.
What is the melting temperature (Tm) of DNA?
The temperature at which half of the DNA molecules in a sample become denatured.
What is a topoisomer?
Different forms of circular DNA that differ only in linking number.
What is a ribozyme?
An RNA molecule with catalytic activity.
What is a G-quadruplex?
A DNA structure consisting of four base-paired guanine residues derived from one, two, or four DNA strands.
Fill in the blank: The process of refolding a denatured protein or nucleic acid chain back to its native structure is called _______.
renaturation
True or False: Histone binding to DNA is sequence-specific.
False
Histone binding does not require a specific combination of nucleotide bases.
