Nucleic acids Flashcards
Draw adenosine 5’ trisphosphate
How would deoxyadenosine 5’ triphosphate be different?
Lack an OH group on the 2’C
How is a purine nitrogenous base linked to the ribose or deoxyribose sugar?
N9 to C1’
How is a pyrimidine nitrogenous base connected to a ribose or deoxyribose sugar?
N1 to C1’
The nitrogenous base of a nucleotide or nucleoside is connected to the C1’ or __________ carbon of the deoxyribose or ribose in the ______ configuration.
Anomeric
Beta
What are the three components of a nucleotide?
- Sugar (ribose or deoxyribose)
- Nitrogenous base (cytosine, adenine, guanine, thymine, uracil)
- Phosphate groups
How is a nucleoside different from a nucleotide?
A nucleoside consists only of the sugar and nitrogenous base; a nucleoside has no phosphate groups attached
What is the name of adenine when bound to ribose?
Adenosine
What is the name of guanine when bound to ribose?
Guanosine
What is the name of cytosine when bound to ribose?
Cytidine
Why is the name of thymine when bound to ribose?
Thymidine
Draw the structure of cytidine 5’ trisphosphate?
Nucleotides play a number of important roles in the cell. What are the four primary ones discussed in class?
- Energy currency (e.g., ATP)
- Secondary messenger (e.g., cAMP)
- Cofactor and metabolic intermediate components (e.g., NAD+, FAD+)
- Nuclei acid building blocks (DNA, RNA)
What is the name of this nitrogenous base?
Adenine
What is the name of this nitrogenous base?
Guanine
What is the name of this nitrogenous base?
Cytosine
What is the name of this nitrogenous base?
Thymine
What is the name of this nitrogenous base?
Uracil
Draw all 5 nitrogenous bases.
Label all possible hydrogen acceptors (A) and donors (D) in the nitrogenous structures.
What is the anatomy of a hydrogen bond (i.e., in terms of acceptor, donor, etc.)?
How would the hydrogen bonding pattern be different if guanine existed in its enol form?
The carbonyl group would become a hydroxyl group; as such, guanine would pair with thymine or uracil
The enol form of guanine is favored at ____ pHs.
Low (acidic)
Enol guanine pairs with _________ and _________.
Thymine
Uracil
Covalent bonds link nucleotides in a 3’-5’-phosphodiester linkage. Draw and/or identify this bond.
Draw the structure of 5’ r-ACG-3’.
Two fundamental differences in DNA and RNA lead to differing ___________.
Stabilities
Which is more stable: DNA or RNA?
DNA
The lack of a 2’ ________ group makes _____ more stable than RNA.
Hydroxyl
In vivo, cytosine can deaminate to ________ spontaneously.
Uracil
What are the two primary reasons DNA is more stable than RNA?
- DNA lacks the 2’ hydroxyl group, which is reactive
- Cytosine can deaminate spontaneously to uracil in RNA, thereby altering base-pair binding
What are the 4 general properies of nucleotides discussed in class?
- Nitrogenous bases are aromatic and roughly planar
- Nitrogenous bases are essentially hydrophobic
- Nitrogenous bases absorb light at 260 nm
- C1’ to N glycosyl bond has two stable conformations with respect to deoxyribose
Deoxyribose has two stable conformations of the C1’ - N glycosyl bond: a _______ and a ______.
Syn
Anti
What is the difference between the syn and anti conformations of deoxyribose nucleotides?
In syn, the nitrogenous base is directly above the sugar
In anti, the nitrogenous base is to the right of the sugar
The syn and anti conformations are only possible in the purines ___________ and _________; they are not possible in the pyrimidines ____________ and ___________ because of _______.
Adenine
Guanine
Cytosine
Thymine
Sterics
Chargaff’s rules determined that in DNA the number of ________ and thymine residues were equal as are the numbers of __________ and guanine residues.
Adenine
Cytosine
Chargaff’s rules established that base pairs hold together ____ complementary strands of DNA often referred to as Watson-Crick pairs.
Two
Most proteins bind in the ____________ groove of DNA.
Major
Base pairs are held together via ____________ bonds.
Hydrogen
There are _____ hydrogen bonds between cytosine and guanine and ___ hydrogen bonds between adenine and thymine, resulting in greater stability of ____ and ___ base pairs.
Three
Two
Cytosine-guanine base pairs
How can you identify the major and minor grooves by looking at base pairs?
The major groove occurs where the backbones are far apart, the minor groove occurs where they are close together
Based on the models of base pairs proposed by Chargaff, along with X-ray crystallographic data by Rosalind Franklin, __________ and __________ proposed the structure of DNA as the __________ ________ in 1953.
Watson and Crick
Double helix
What are the 5 structural features of the Watson-Crick double helix?
- Nitrogenous bases occupy the core
- Sugar-phosphate backbone occupies the exterior surface and contains two groovese of unequal width
- Hydrogen bonding between complementary base pairs results in specific association of two chains of the double helix
- Base stacking interactions stabilize the double helix
- Two strands run in antiparallel directions and form a right-handed double helix
Complementary strands are not __________.
Identical
Guanine-cytosine strands are more stable not because they have three hydrogen bonds, but because of _______ _______.
Base stacking
What is base stacking?
Base stacking refers to pi system electrostatic interactions from aromatic bases stacked on top of one another in the DNA double helix
Write the complementary DNA sequence to the following sequence: AGCTATAA
3’ TCGATATT 5’
DNA exists predominantly in nature in _________ ________ form.
Double stranded
Double stranded helical structures can adopt a number of stable structures. In class, we discussed three conformations of double stranded DNA: __________, ___________, __________.
A form
B form
Z form
Which form of DNA is the Watson Crick model?
B form
What are the identifying features of the A form of DNA?
Short, squatty
Narrow and deep major groove
Very broad and shallow minor groove
What are the identifying features of B DNA?
Long and thin
Wide major groove
Narrow minor groove
What are the identifying characteristics of Z DNA?
Sugar-phosphate background is zig-zag
Flat major groove
Narrow minor groove
Which forms of DNA are right-handed?
A DNA
B DNA
Which forms of DNA are left-handed?
Z DNA
How many base pairs occur per turn in A DNA, B DNA, and Z DNA?
11
10.5
12
What are the tilt degrees in the three forms of DNA?
A DNA: 20 degrees
B DNA: 6 degrees
Z DNA: 7 degrees
Which form of DNA has the most base pairs per turn?
Z DNA
Which form of DNA has the largest title angle?
A DNA
Order the diameter sizes of the three forms of DNA from smallest to largest.
Z form (18 Angstroms) < B form (20 Angstroms) < A form (26 Angstroms)
The sugar pucker of A DNA is C3’ ____ or the same said as C5’ whereas the sugar pucker of B DNA is C2’ ____ or the same side as C5’.
Endo
Enco
Both A and B DNA have endo sugar puckers, but A DNA has a ____ endo pucker and B DNA has a C2’ endo pucker.
C3’
Z DNA also shows sugar puckering, but the sugar puckering pattern is different for pyrimidines and purines. Pyrimidines are C2’ endo while purines are _____ endo.
C3’
Both A and B DNA have glycosyl bond conformations in the ______ position while Z DNA has two glycosyl bond conformations depending upon the nitrogenous base: _____ for purines and _____ for pyrimidines.
Anti
Syn
Anti
Under what 3 conditions is A DNA important?
- Dehydration
- RNA/DNA hybridization
- dsRNA
B DNA is important under ____________ conditions.
Normal
Z DNA is important under 2 conditions. What are they?
- Synthetic sequence, alternating GCGCGC at high salt concentrations
- Gene regulation (B DNA can form Z DNA, functioning as a switch for gene expression)
Be sure you can identify the types of DNA conformations by sight.
Many proteins interact with DNA via the major groove. Show an asparagine residue interacting with the major groove.
Regulatory proteins interact with and recognize DNA via the __________ groove.
Major
Due to its double-stranded nature, DNA can be denatured. What are four ways in which DNA can be denatured?
- Heat
- Ionic conditions (i.e., salt)
- pH
- Urea, formamide
Melting of DNA can be monitored via UV spectroscopy at an absorbance of _____ nm. The DNA sequence determines the Tm, which is the temperature at which half of DNA is double stranded and half of DNA is single stranded.
260 nm
More guanine and cytosine pairs in DNA will shift the Tm to the ________ (right or left)?
Right
It will require more heat to separate strands; therefore, it will have a higher Tm
DNA denaturation is a _______________ process, resulting in a ________________ (sigmoidal or hyperbolic) UV spectrum.
Cooperative (all-or-nothing)
Sigmoidal
What is the hyperchromic effect?
Absorance increases as bases unstack (denature) in DNA
As DNA denatures, absorbance ____________ (increases or decreases), and as DNA anneals, absorbance _________ (increases or decreases) due to the __________________ effect.
Increases
Decreases
Hydrochromic effect
Denatured DNA has a ________ viscosity than annealed DNA.
Lower
Each DNA has a characteristic melting temperature or Tm, the temperature at which ______ of the DNA strand is in a random coil or double strand and the other ______ is ______.
50%
50%
Single-stranded
Re-forming dsDNA is called ______________.
Annealing
Annealing can be ______________ if the denaturant is removed, unlike most proteins.
Spontaneously
DNA damage can occur when DNA is exposted to ____ radiation or __________ chemicals. One such class of products are called ____________ agents. They alter certain bases of DNA.
UV radiation
Reactive chemicals
Alkylating agents
Alkylating agents add _____ groups to nitrogenous bases, which can disrupt base pairing and lead to DNA _______ and even ________.
Alkyl groups
DNA damage
Cancer
One type of alkylating agent discussed in class is ____, which converts an enol guanine to an O6-methylguanine, which does not effectively pair with cytosine.
OMS
How does the structure of RNA differ from DNA?
- RNA is usually single-stranded, but…
- RNA can adopt a variety of 3D structures (e.g., step loop, hairpin)
- RNA can act as an enzyme (e.g., ribozyme)
RNA often contains non-Watson-Crick base pairs. Draw the hydrogen bonding pattern that would occur in a guanine:uracil base pair (sometimes called a wobble base pair).
