Chapter 2 Flashcards
What is the primary structure of DNA?
Nucleic Acid – Long chain or polymer of repeating subunits
DNA is composed of nucleotides that form a long chain.
What are the components of a nucleotide?
Composed of:
* Five-carbon sugar
* Phosphate group
* Nitrogen-containing, heterocyclic base
Nucleotides are the building blocks of nucleic acids.
What is the role of the ribose ring in nucleic acid strands?
Imparts direction to a DNA/RNA nucleic acid strand
The directionality is crucial for processes like replication and transcription.
What is the main difference between RNA and DNA?
The presence of a 2’ hydroxyl group in RNA
This hydroxyl group makes RNA more reactive and less stable than DNA.
What are Edwin Chargaff’s rules?
- [A] = [T]
- [G] = [C]
- [A] + [G] = [T] + [C]
These rules describe the base pairing in DNA and are fundamental to the structure of DNA.
How does GC content vary among species?
%G+C differs among species but is constant in all cells of an organism within a species
GC content can range from 22% to 73% among different species.
Fill in the blank: The percentage of G+C in DNA varies from ______ among species.
22 to 73%
This variation is a characteristic feature of different organisms.
What does the phosphate functional group give?
Gives DNA acidic properties
What are the steps to assemble the components?
- Nitrogenous base is covalently linked to one
molecule of sugar at the 1’ carbon of the sugar -
Nucleoside - A nucleoside with one or more phosphates
attached is a nucleotide. - Nucleotides are linked by 5 to 3′ ′
phosphodiester bonds between adjacent
nucleotides to form a DNA or RNA chain
What are the distinct ends of a DNA or RNA chain?
5 -PO′ and 3 -OH ends
These ends have different properties.
How is a DNA sequence conventionally written?
With the 5 end to the left and the 3 end to the right
This is a standard notation in molecular biology.
What unit is used to measure the length of RNA?
Number of nucleotides (nt) or bases
This quantifies the RNA length.
What unit is used to measure the length of double-stranded DNA?
Number of base pairs (bp)
Each base pair corresponds to two nucleotides.
How many base pairs are in 1 kilobase pair (kb or kbp)?
1000 bp
Kilobase is a common unit in genetics.
How many base pairs are in 1 megabase pair (Mb or Mbp)?
1,000,000 bp
Megabase is often used to describe large DNA sequences.
What are oligonucleotides?
Short chains of single-stranded DNA (< 50 bases)
Oligonucleotides are often used in PCR and other molecular techniques.
What type of bonds join successive deoxyribose residues in a polynucleotide chain?
Phosphodiester bonds
These bonds form the backbone of DNA and RNA.
Where is the free 5 end located in a polynucleotide chain?
At one end of the chain (conventionally the left)
This end has a phosphate group.
Where is the free 3 end located in a polynucleotide chain?
At the other end of the chain
This end has a hydroxyl group.
What structure do two complementary strands of DNA form?
Double helix
What stabilizes the two strands of DNA together?
Base pair hydrogen bonding and base stacking
How many hydrogen bonds form between adenine (A) and thymine (T)?
Two hydrogen bonds
How many hydrogen bonds form between guanine (G) and cytosine (C)?
Three hydrogen bonds
What are the two common ‘Watson-Crick’ base pairs in DNA?
- Adenine (A) with Thymine (T)
- Guanine (G) with Cytosine (C)
Why are there no other stable base pairs present in DNA?
- May not form two or more hydrogen bonds
- Pairing of G with T produces a shape similar to Watson-Crick pairs
What mechanisms ensure fidelity of DNA replication?
Proofreading and DNA repair mechanisms
True or False: RNA more readily uses alternative base pairing than DNA.
True
Fill in the blank: A-T base pairs can form _______ hydrogen bonds.
two
Fill in the blank: C-G pairs form _______ hydrogen bonds.
three
What is the core structure of double stranded DNA?
A hydrophobic core
This hydrophobic core is crucial for the stability of the DNA structure.
What are the characteristics of the heterocyclic bases within DNA?
Nonpolar, hydrophobic, and relatively flat rings
These characteristics contribute to base stacking.
How does base stacking contribute to DNA structure?
By excluding water from the core of the double helix
This exclusion enhances the chemical stability of DNA.
What provides chemical stability to the DNA double helix?
Base stacking
The stacking occurs through the flat, hydrophobic nitrogenous bases.
Describe the arrangement of nitrogenous bases in DNA.
Stack onto each other without a gap by means of a helical twist
This arrangement is critical for the structural integrity of the DNA.
What are the two types of grooves formed in the DNA double helix?
Major groove and minor groove
The major groove is wider and more exposed than the minor groove.
Which groove of DNA is typically more exposed and readable?
Major groove
The sequence in the major groove can be recognized by proteins and other molecules.
In which form is DNA schematically represented?
B form
This is the most common form of DNA in cells.
What are some alternative structures to the B form of DNA?
A form, Z form, B’, C, C’
These structures vary in helical width, handedness, and groove shapes.
What is the polarity direction of each DNA strand?
5′ to 3′
This polarity is crucial for DNA replication and function.
How are the two strands of DNA oriented in relation to each other?
Antiparallel
This orientation is essential for the base pairing mechanism.
What are the two key features of the Watson-Crick DNA double helix?
Complementary base pairs and base stacking
These features are fundamental for the stability and replication of DNA.
What are the two features that make DNA a useful molecule for the transmission of hereditary information?
- The sequence of nucleotides can be exceptionally complex.
- It can be replicated by unwinding the two strands of DNA.
What is the significance of a sequence of 10 nucleotides in DNA?
It could exhibit 410 (or about a million) different combinations of nucleotide bases.
What type of bonds hold each single strand of DNA together?
Covalent bonds.
What type of bonds hold the two strands of DNA together?
Weaker bonds, including base stacking and hydrogen bonds.
What is DNA denaturation?
Unwinding and separation of DNA strands.
How can DNA denaturation be monitored in vitro?
By absorbance spectroscopy.
What is Tm in the context of DNA?
The temperature at which half of the bases in a dsDNA sample have denatured.
What phenomenon occurs as DNA melts and absorbs UV light?
Hyperchromicity.
What are two factors that can change the way DNA denatures?
- G/C content within a strand of DNA
- Salt concentrations.
What is renaturation or reannealing of DNA?
The process by which denatured DNA can anneal, allowing for hybridization.
What is hybridization in the context of DNA?
The complementary base pairing of strands from two different sources.
What factors affect the rate at which DNA reanneals?
- Length of the DNA
- Initial concentration in the sample.
What are some examples of unusual DNA secondary structures?
- Slipped structures
- Cruciform structures
- Triple helix DNA
- G-quadruplex.
True or False: The extent of unusual DNA secondary structures occurring in vivo is well understood.
False.
What are slipped structures?
Structures that occur in sequences of short tandem repeats
Slipped structures can lead to mutations and are associated with certain genetic disorders.
What is required for loops to form in DNA?
Loops need to form in both strands of DNA
Which diseases are associated with trinucleotide expansions?
Huntington’s disease and Myotonic dystrophy
What are cruciforms?
Structures that occur at DNA sequence palindromes or inverted repeats
Cruciforms result from the formation of stem-loop structures.
What is the structure of a cruciform?
Formed due to the formation of a stem loop structure in the strands of DNA
What are triple helices in DNA?
A more complex structure facilitated by mirror repeats
A third single strand associates with a double-stranded DNA molecule.
What happens to the strands of DNA in a triple helix?
Wraps into the major groove, leaving one strand single stranded
What are the symptoms of Friedreich’s ataxia?
Loss of voluntary muscular coordination and heart enlargement
What trinucleotide repeat is expanded in Friedreich’s ataxia?
5 -GAA-3′ ′ trinucleotide repeat expansion
What is the normal range of GAA repeats in individuals?
6-34 repeats
What is the range of GAA repeats in Friedreich’s Ataxia?
66-1700 repeats
What structure is formed by expanded GAA repeats?
Triple helix DNA
What is a G-quadruplex?
A four-stranded DNA structure in a stretch of tandem guanines
What is formed within a G-quadruplex?
G-tetrad
What roles do G-quadruplexes play in the genome?
Gene regulation and genomic instability
Where are G-quadruplexes commonly found?
In telomeres and promoter regions
What is supercoiling of DNA?
Supercoiling conserves cellular space and can store energy
Supercoiling can be negative or positive, affecting the stability and functionality of DNA.
Is relaxed DNA supercoiled?
No
Relaxed DNA does not have supercoils.
What is a negative supercoil?
Results from underwound DNA
Negative supercoiling is common in cellular DNA.
What does a positive supercoil result from?
Results from overwound DNA
Positive supercoiling is associated with processes like DNA replication.
What is the linking number (L) in DNA?
Number of times two hydrogen bonded strands of DNA cross each other
L remains constant despite changes in supercoiling.
What does ‘twists’ (T) refer to in DNA?
Number of twists/turns in a segment of DNA
T changes with supercoiling.
What are two reasons for negative supercoiling in DNA?
- Space saving
- Puts energy into the DNA molecule
Negative supercoiling facilitates unwinding of DNA for replication and transcription.
What is the typical state of DNA in prokaryotes and eukaryotes?
Virtually all DNA is negatively supercoiled
This state is crucial for various cellular processes.
What happens to the linking number (L) when transitioning from a supercoiled state to a relaxed state?
The change is negative
Example: 9 – 10 = -1.
When does positive supercoiling occur in vivo?
- During DNA replication
- During transcription
Positive supercoiling must be released for these processes to succeed.
What role do topoisomerases play in DNA supercoiling?
Catalyze the release of supercoiling by producing breaks in the DNA
This allows turns to be added or subtracted from the helix.
How does negative supercoiling facilitate DNA processes?
Makes it easier to separate DNA strands during replication and transcription
It also puts energy into DNA and aids in packaging.
What state does the DNA of thermophilic Archaea exist in?
Positive supercoiled state
This protects DNA from denaturation at high temperatures.
DNA structure overview:
Primary, secondary, and tertiary
Primary: Nucleotide structure, nucleotides joined by phosphodiester bonds
Secondary: Double helix, B-DNA, Unusual structure
Tertiary: Supercoiling
