Lecture 3: Nucleic Acids Flashcards
Chemical name for 1 phosphate?
Label the structure!
Monophosphate
Monomeric units w/ phosphates?
Nucleotides
Monomeric units that lack phosphates
Nucleosides
Label the Nucleotide!
How would it be different for DNA vs RNA?
Two ______ bases: DNA and RNA contain A & G.
Two Purine bases: DNA and RNA contain A & G.
Name the base.
Name the base.
3 _______ bases: DNA and RNA contain C;
mainly T in DNA;
mainly U in RNA.
3 Pyrimidine bases: DNA and RNA contain C;
mainly T in DNA;
mainly U in RNA.
Name the base.
Name the base.
DNA/RNA?
DNA
Name the base.
DNA/RNA?
RNA
Where does the Glycosidic Bond attach for Purines?
Pyrimidines?
Purines: At N9 to sugar at C1’
Pyrimidines: At N1 to sugar at C1
Name the Deoxyribonucleotide.
Symbols?
Nucleoside?
Name the Deoxyribonucleotide.
Symbols?
Nucleoside?
Name the Deoxyribonucleotide.
Symbols?
Nucleoside?
Name the Deoxyribonucleotide.
Symbols?
Nucleoside?
Name the Ribonucleotide.
Symbols?
Nucleoside?
Name the Ribonucleotide.
Symbols?
Nucleoside?
Name the Ribonucleotide.
Symbols?
Nucleoside?
Name the Ribonucleotide.
Symbols?
Nucleoside?
What is this compound?
Nucleoside?
Nucleotides?
Adenosine Triphosphate
Nucleoside: Adenosine
Nucelotides: AMP, ADP, ATP
Name the structure and phosphate.
Adenosine (Adenosine diphosphate, ADP)
Inorganic Phosphate
Name the structure and phosphate.
Adenosine (Adenosine monophosphate, AMP)
Inorganic Pyrophosphate
What types of substrates does DNA & RNA require?
dNTP, NTP
DNA Secondary Structure was founded by whom and when?
Chargaff, 1950
Chargaff’s Rules for DNA Secondary Structure:
- All ______ in the ______ species have the ___ mol-% of all _ nucleotides.
- mol-% of _____ = mol-% of _____
- %A = %___ and %G =%___
- i.e. A+G =___+_____
- W-C MODEL: A pairs w/ ___ and G pairs w/ ___, and same ____ in all cells
Chargaff’s Rules for DNA Secondary Structure:
- All tissues in the same species have the same mol-% of all 4 nucleotides.
- mol-% of Purines = mol-% of Pyrimidines
- %A = %T and %G =%C
- i.e. A+G =T+C
- W-C MODEL: A pairs w/ T and G pairs w/ C, and same DNA in all cells
What is the backbone of DNA Secondary Structure according to Chargaff and where does new dNTP and NTP get added?
Phosphate-deoxyribose backbone
3’ end of growing polynucleotide chain
According to the Watson-Crick Model, what type of backbone encompasses the nucleotides?
________ bases (paired by H-Bonding) on the inside – base-pairs are stacked on one another with planes ____ to the helix axis.
Hydrophilic phosphate-deoxyribose backbone
Hydrophobic bases (paired by H-Bonding) on the inside – base-pairs are stacked on one another with planes perpendicular to the helix axis.
According to the Watson-Crick Model, complimentary strands run ________.
A-T has __ H-Bonds.
G-C has __ H-Bonds.
Which complimentary pair is is stronger?
According to the Watson-Crick Model, complimentary strands run antiparallel.
A-T has 2 H-Bonds.
G-C has 3 H-Bonds, hence the stronger bond.
What form of DNA is a right-handed double helix, forms when fully hydrated and under conditions in vivo w. majority of proteins recognizing the major groove?
B-Form
The B-form of DNA is a highly (+/-) molecule and every base needs __ phosphodiester bond(s).
The B-form of DNA is a highly - molecule and every base needs 1 phosphodiester bond.
The B-form of DNA us a right-handed double helix model that is stabilized by:
- ________ interactions: base stacking
- __-Bonding between Pu—Py
- ______: neutralize the (-) on the phosphates along the helix of DNA
The B-form of DNA us a right-handed double helix model that is stabilized by:
- Hydrophobic interactions: base stacking
- H-Bonding between Pu—Py
- Cations: neutralize the (-) on the phosphates along the helix of DNA
What form of DNA forms under dehydrated, non-physiological conditions; right-handed helix?
A-DNA
What form of DNA is rich in GC content, left-handed, and is important in protein recognition & gene regulation?
Z-DNA
Why does DNA need to be condensed and how does it fold?
To fit into cells, Linearly
in eukaryotic cells, DNA is wrapped around proteins called ________ to help package it in cells.
in eukaryotic cells, DNA is wrapped around proteins called histones to help package it in cells.
DNA bases can be modified to provide additonal level to the “code” = _______
DNA bases can be modified to provide additonal level to the “code” = epigenetics
What is the loss of structure of DNA & proteins by melting w/ high heat, causing interaction of H-bonds and the chains to come apart?
Denaturation
In what does the duplex melt (no covalent bonds break)?
- ?
- ?
- ?
In what does the duplex melt (no covalent bonds break)?
- Acid
- Alkali
- Heat
Stability/melting temperature (Tm) a function of _/_ content because they contain _ H-bonds.
Stability/melting temperature a function of G/C content because they contain 3 H-bonds.
What is the reassociation of denatured DNA strands?
And at what temp stability/melting temp is ideal?
Annealing
~25º C below Tm
High ____ stabilizes the duplex, increasing Tm, due to
- __________ interactions (bp’s)
- ________ shielding
High salt stabilizes the duplex, increasing Tm, due to
- Hydrophobic interactions (bp’s)
- Phosphate shielding
What determines the DNA and melting temperature (denaturation) for a molecule and why?
Amount of G/C content, due to the amount of H-bonds (3 in GC)
What type of group is RNA secondary structure?
2’ OH group
T/F: Does RNA have a simple, regular secondary structure?
False
What are the most common secondary structures for RNA?
A-form double helices and hairpins
Ribose 2’ OH of RNA causes _____ interactions in base stacking that prevent _____ of more than 10-12 bp’s.
Ribose 2’ OH of RNA causes steric interactions in base stacking that prevent coils of more than 10-12 bp’s.
Steps of DNA duplication:
- ____ copies 3 nucleotide codon (_RNA)
- _RNA reads encoded gene information from _RNA
- _RNA transfers appropriate ____ ____ to a growing polypeptide chain for protein synthesis
Steps of DNA duplication:
- DNA copies 3 nucleotide codon (mRNA)
- tRNA reads encoded gene information from mRNA
- tRNA transfers appropriate amino acid to a growing polypeptide chain for protein synthesis
