DNA Lecture 1 Flashcards
type of RNAs that are a component of
ribosomes
rRNAs
type of RNAs that are intermediaries,
transmitting genetic information from the site of
DNA in a cell (primarily the nucleus) to the site of
protein synthesis in the cell (ribosome).
mRNAs
Type of RNAs that are adapter molecules,
translating the information in mRNA into a
specific amino acid sequence
tRNAs
The repositories and
transmitters of genetic information for every
cell, tissue and organism
nucleic acids
nucleic acids are polymer chains with
similar monomers (called nucleotides) connected
by
covalent bonds
What are the three characteristic components of nucleotides
1) A phosphate group
2) A five-carbon sugar
3) A heterocyclic nitrogenous base
What are the five carbon sugars in RNA and DNA?
beta-D-ribose in RNA
beta-2’-deoxy-D-ribose in DNA
The molecule in RNA/DNA without the phosphate group is called the
nucleoside
The numbered carbon atoms of the ribose component in the nucleotides are given a prime (‘) designation to distinguish them from the numbered atoms of the
Nitrogenous base
In DNA nucleotides, the C-2 hydroxyl group of ribose in replaced by…(called 2-deoxy)
A hydrogen atom
refers to the stereochemical configuration of C-1 (anomeric carbon) in the cyclic form of 2-deoxy-D-ribose. Note that the OH on the C-1 is on the same side of the ring as C-5
β
Refers to the stereochemical configuration of the C-4 (penultimate carbon). It has the same configuration as D-glyceraldehyde
D
Ribose is an _____ because it has an aldehyde group
Aldose
In _______, the straight chain (aldehyde) and ring (β-furanose) forms of free ribose are in equilibrium
Solution
In _______, both types of pentoses are in their β-furanose form (closed-five membered ring)
Nucleotides
n solution, all monosaccharides with five or more carbon atomsin the backbone occur predominantly as cyclic (ring) structures in which the carbonyl group forms a ____ with the oxygen of the hydroxyl group along the chain
covalent bond
The cyclic hemiacetal form that results from intramolecular reaction of the the C-4 OH group with the C-1 aldehyde group
D-ribose
The anomeric carbon (C-1) is the
The chiral carbon that is most distant from the carbonyl carbon is the
Hemiacetal carbon
Penultimate carbon
Is the pentose ring planar?
No, it has puckered conformations
The bases in nucleotides can be characterized as ___ and _____
purines and pyrimidines
Bases in nucleotides that are monocyclic nitrogen heterocycles
Pyrimidines
Bases in nucleotides that are bicyclic nitrogen heterocycles
Purines
Both DNA and RNA contain two major ____ bases:
Purine, Adenine (A) and Guanine (G)
DNA and RNA also contain two major _____ bases
For DNA, they are
pyrimidine
cytosine and thymine
cytosine and uracil
Why are purines and pyrimidines referred to as bases?
The NH2 and or ring nitrogen atoms are weakly basic, the lone pair of electrons on the nitrogen atom can accept a proton in an acid-base equilibrium
Another characteristic of nucleotide bases is that they can exist in other ______ forms
There reaction equilibria favors the ____ and _____ forms (they are the most stable)
tautomeric
amino and keto
Tautomeric forms of nucleotide bases have different ______ characteristics
H-bonding
N-1 of adenine is an H-bond _____ in the amino form, but an H-bond ____ in the imino form
acceptor
donor
The keto oxygen on C-4 of thymine can as as an H-bond ______ while the nol form can act as an H bond ______
acceptor
donor
Why is hydrogen bonding so important in nucleotide bases?
H-bonding of amino and keto forms of the bases allows a complimentary association of two strands of DNA
What are the complimentary base pairs in DNA and RNA?
DNA: A-T , C-G
RNA A-U, C-G
Since the imino form of A can’t form H-bonds with the keto form of T in the same way, spontaeneous ___ can result from the formation of abnormal base pairs
mutations
The purines and pyrimidines are what kind of molecules?
Aromatic
Electron delocatlization among ring atoms or purines and pyrimidines results in most of the bonds having partial…
double bound character
Pyrimidines are nearly planar/planar
purines are nearly planar/planar
planar
nearly planar
Are purines and pyrdimidines hydrophilic or hydrophobic?
Are they soluble or insoluble in water at the cell pH (near neutral)?
Hydrophobic
insolube
Bases are covalently bonded to ribose or deoxyribose in an N-β - glycosyl bond to the ___ carbon of the pentose ring
1’
The bonding of bases to ribose or deoxyribose occurs where on pyrimidines?
Where on purines?
N-1 of pyrdimidines
N-9 of purines
The N-β-glycosyl bond is formed by removal of the elements of..
The resulting structure (ribose or deoxyribose with base attached) is called a
Water (OH from pentose and H from heterocyclic base)
Nucleoside
When a phosphate is _______ to the 5’ carbon of the pentose ring with base attached, the resulting structure is a
esterified, nucleotide
The nucleotides are linked together by ____ t0 _____ phosphodiester bonds to form a linear polmer
5’ to 3’ phosphodiester bonds
The covalent backbones of nucleic acids consist of alternating phosphate and pentose residues
The nitrogenous bases may be thought of as side groups joined to the backbone at regular intervals
!
The polymer chain at the terminal nucleotide at the 5’ end has a free ________ group
The terminal group at the 3’ end has a free
5’ phosphate group
3’ OH group
When the phosphate group forms a diester linkage, there’s on ionizible oxygen shown in the ionized form. Why is phosphodiester in the ionized form?
Phosphoric acid is a tribasic acid that has 3 ionization equilibria…
The ionization of the phosphodiester group found in a nucleic acid corresponds to a pKa ~ 1.4
Based on this pKa, the unionized form of a polymer of nucleotides would be a strong acid
The ionized form of a polymer of nucleotides with the negative charge on the phosphate oxygen will exist almost exclusively at pH =
7.0
