Flashcards in Lecture 1 - Nucleotides and DNA Deck (79):
What are the 3 parts of a nucleotide?
1. Purine or pyrimidine base
2. Pentose sugar
3. Phosphate group
What forms the backbone of DNA?
Phosphoester linkages between phosphate groups and sugars
Order of DNA?
5' => 3'
How to differentiate between purines and pyrimidines?
Longer name = smaller structure
2. Thymine (DNA)
3. Uracil (RNA)
On what part of nucleotides do mutations happen most often on?
What is a nucleoside?
Base + sugar
What is a nucleotide?
Base + sugar + phosphate
What are deoxyribonucleotides?
Nucleotides with β-2′-deoxy-D-ribofuranose (without a 2' (-OH) group)
What are deoxyribonucleotides used for?
What are ribonucleotides used for?
Order of DNA synthesis?
5' => 3'
How many H bonds between A and T?
How many H bonds between C and G?
Why is the antiparallel structure of DNA more thermodynamically favorable/stable?
Because it orients the H bonds in a linear manner, in which they are the strongest
How was the DNA structure discovered?
By X-ray showing the diffraction pattern of DNA: spots forming a cross in the center denote a helical structure and heavy bands at the left and right arise from the recurring bases
Periodicity of the helical structure? What does it represent?
34 angstroms (36 in solution) = periodicity of the stacking of the bases
Which noncovalent bond is the strongest in the presence of water?
Van der Waals
If the H bonds contribute so significantly to the stability of DNA, then what must be true about the interior of the helix?
Water is excluded
What does the 5' end of DNA/RNA lack?
A nucleotide at the 5′ position
What does the 3' end of DNA/RNA lack?
A nucleotide at the 3′ position
Is the backbone of DNA/RNA polar?
What is the sugar of RNA? How does it exist in solution?
β-D-ribofuranose: the straight-chain (aldehyde) and ring (β-furanose) forms of free ribose are in equilibrium (99% ring form)
What happens to DNA when put in solution?
B to A form
What is semi-conservation replication of DNA?
The preexisting or "parent" strands become separated, and each is the template for biosynthesis of a complementary "daughter" strand
What are the 3 forms of DNA? Most common one? Least common one?
2. B (most common)
3. Z (least common)
Helical sense of A form DNA?
Helical sense of B form DNA?
Helical sense of Z form DNA?
A form: base pairs per helical turn?
B form: base pairs per helical turn?
Z form: base pairs per helical turn?
What was the most significant finding of the Watson-Crick model for the structure of DNA?
B form: angstroms per base?
A form: angstroms per base?
Z form: angstroms per base?
What form does double stranded RNA take?
What do all DNA forms have in common?
Major and minor grooves
A form: diameter?
B form: diameter?
Z form: diameter?
More unstable form of DNA?
Reads the same 5' to 3' on each different strand
DNA mirror repeat?
Reads the same 5' to 3' and 3' to 5' on same strand
What is a hairpin?
Secondary structure of palindromic SINGLE stranded DNA (or RNA) sequences formed by intrastrand base pairing
How to superimpose palindromic sequences?
Must be rotated 180˚ about the horizontal axis then 180˚ about the vertical axis
How to superimpose mirror repeat sequences?
Requires only a single 180˚ rotation about the vertical axis
What is a cruciform?
Secondary structure of palindromic DOUBLE stranded DNA (or RNA) sequences formed by intrastrand base pairing
Role of hairpins and cruciforms?
Regulatory sequences or DNA binding domains
What is a Hoogsteen base pair? What does it imply?
Alternative base pairing
Means we can have a triplex or tetraplex DNA
Are Hoogsteen base pairs pathological?
Are triplex and tetraplex forms of DNA parallel or antiparallel?
What is particular about triplex DNA segments in vivo?
They are very short
What is the 3rd strand of triplex DNA called?
Triplex-forming oligonucleotide (TFO)
Is the TFO DNA or RNA?
Can be both!
To what do DNA binding proteins bind?
Double stranded DNA
What do Hoogsteen nucleotides and DNA binding proteins have in common?
They bind to DNA in the minor and major grooves
What could be a possible role for triplex DNA segments?
May regulate transcription (or even replication) by:
1. Blocking binding of transcriptional factors
2. Blocking elongation by being downstream of transcriptional start site
How can triplex sequences be identified experimentally?
Immunofluorescent monoclonal antibodies
What is the role of human replication proteins A? 2 examples?
They melt and disrupt DNA triplex structures
Jel 466 and DAPI
What could be a reason why DNA is the genetic language instead of RNA?
Maybe because RNA duplexes are unable to accommodate Hoogsteen base pairing, which may make DNA more stable than RNA because when mutations happen, DNA can flip the base so that a Hoogsteen pairing happens inside the helix until full repair happens ==> DNA can better accommodate mutations
What pattern does single stranded RNA form?
Typical right-handed stacking pattern
Which is more stable: double-stranded DNA or RNA? How come?
RNA, most likely because of ribose
What are 3 tertiary structures of RNA?
3. Ribozyme intron
Which reforms faster: denatured DNA or proteins? Why?
DNA because only 4 bases compared to 20 AAs
What does the melting temperature of DNA represent?
Temp at which you've lost 50% of the standard shape
What increases the melting temp of DNA? Why?
Higher G-C content because 50% more H bonds
Describe the relationship between G-C content and melting temp of DNA.
DNA melting temp with 0% G-C?
Below 70 degrees Celcius
What do DNA regions high in A-T content represent? What is this called?
Likely to be separated therefore points at which transcription bubbles and replications forks can be most easily inserted = DNA breathing
Describe the geometry of the bases.
Name of A nucleoside?
Name of A nucleotide?
Which DNA form corresponds the most to the model made by Watson and Crick?
Is DNA denaturing via salt or high temps relevant in vivo?
Nope, only happens in the lab
Watson-Crick model: how many base pairs and angstroms per turn of the helix?
10 base pairs, or 34 Å (3.4 nm), per turn of the helix
What does the melting temp of DNA depend on? 2
1. pH and ionic strength
2. Size and base composition of the DNA