Complete List of Terms and Definitions for Nucleotides and Nucleic Acids 2

Terms Definitions
pyrimidine derivative dihydrouracyl
cytosine -2-oxy-4-amino pyrimidine
The nitrogenous base that makes three hydrogen bonds with guanine.
DNA picture perfect
GMP -guanosine 5'-monophosphate
-guanylic acid
Nucleotides can be __3_things__? Monophosphate
tRNA -small polynucleotide chains
-several bases usually methylated
-each a.a. has at least one unique tRNA
-3'-terminal sequence is always CCA-a.a.
-aminoacyl tRNA are substrate of protein synthesis
-5 tRNA can carry Leu
-contain anticodon
thymine -2-oxy-4-oxy-5 methyl pyrimidine
-only found on DNA
-The complementary base to adenine
rRNA modified base structure
Pyrimidines cytosine, uracil, and thymine
Replication: DNA -> DNA
Transcription: DNA -> RNA
Translation: RNA -> protein
Where does transcription takes place? nucleus
EcoRI -sequence GAATTC
-when it find sequence it causes a staggered, double-stranded break by hydrolyzing each chain between the G and A residues
-staggered cleavage leaves strand with 5' sticky ends
-there can be recombination
-first restriction enzyme found in the R strain of E. coli
Deoxyribonucleoside and Deoxyribonucleotide of guanine deoxyguanosine & deoxyguanosine-5'-monophosphate (dGMP)
Nucleotide's base function -division of labor
-information symbol, telling what metabolic fxn each nucleotide should do
-biochem reaction uses phosphate or pyrophosphate group transfer, but sugar and base are left out of it
-info symbol extends to nucleic acids, where it serve as info symbol for genetic info.
Which base does not undergo tautomerism? adenine
DNA structure -anti parallel double helix
-diameter of 2 nm
-DNA size represented by # of nucleotides base pair
-length of 1.6 million nm in E. coli
-compact and folded, very long and easily shredded into shorter fragments during isolation
-eukaryotic DNA wrapped around histone to form nucleosomes
-base pairs A:T, C:G
pyrimidine -single ring, 2 N atoms
-aromatic, planar
-number clockwise
-cytosine, thymine, uracil
-found in DNA, RNA
-bound to sugar and phosphate
Nucleotide nitrogenous base + sugar + phosphate
Nucleotides -when phosphoric acid is esterified to a sugar -OH group of a nucleoside.
-OH group avail. in ribose ring C-2',C-3', C-5'
-OH group avail in d-ribose ring C-3', C-5'
-majority of monomeric nucleotides in cell are ribonucleotides
Nucleic acid hydrolysis -break bond in nucleotide backbone
-important to manipulate polymer molecules
RNA types -mRNA, tRNA, siRNA, rRNA
cells contain up to 8x more RNA than DNA
-siRNA only found in eukaryotic cells
Two basic kinds of nucleic acid DNA, RNA
ΔG°' for hydrolysis of phosphoester about -3.0 kcal/mole
α linkage phosphoester linkage (sugar alcohol + acid)
Origin of replication Where the DNA begins to unwind
Six-cutter -enzymes such as EcoRI or BamHI, will find their unique hexanucleotide sequences on the average once in every 4096 (4^6)bp
-the fragments generated by it are approximately the size of prokaryotic genes. This property makes these enzymes useful in the construction and cloning of genetically useful recombinant DNA molecules.
NDP and NTP -addition of phosphate groups to phosphoryl group of nucleotide through formation of phosphoric anhydride linkage
-groups are α,ß,ϒ
-linkage readily hydrolyzed by acid, liberating inorganic PO3- (P_i))and NMP
-α the group bound to pentose
-occur in the free state in cell
-for deoxy: dAMP>>dADP>>dATP
-there is uracil derivatives for DNA but not Thymine derivative for RNA
Nucleoside 5'-Triphosphates Functions -indispensable agent in metabolims due to phosphoric anhydride bonds they possess, they are prime source of chemical energy to do biological work
-all four NTPs and their dNTPs are substrate for synthesis of nucleic acid
Semiconservative Each new dsDNA has one parental and one new strand
DNA renaturation (annealing) ssDNA + complementary ssDNA --> dsDNA
Where does phosphodiester linkage occur? Links nucleotides 3' to 5'
N-glycosidic bond anomeric C-1' to N-1 or pyrimidine or N-9 or purine
-always beta conformation in nucleoside
Where base pairs in DNA double helix arises from? hydrogen bonds
Naming Restriction Enzyme -3 letter italicized cond
1st letter = genus
2nd and 3rd = species
following letter denotes strain
mRNA in Eukaryotes -DNA- like RNA
-A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.
-first synthesized into large precursor in the nucleus called heterogeneous nuclear RNA, hnRNA.
-introns, exons and contain poly(A) tails
-alternative slicing is 50% or more
What are the general characteristics of Z form DNA? --left-handed structure
--longer and thinner than B form
--shallow major groove
--narrow, deep minor groove
--been proposed to play a role in gene expression and recombination
Why does DNA contain thymine -cytosine naturally deaminates to form uracil
-cell would not have any way of knowing whats a mutated C and a regular U
-thymine is a (5-methyl-U) to solve this problem, if cythosine becomes U then repair enzyme knows DNA has no U.
What consequence does the antiparallel orientation have on DNA structure? antiparallel orientation allows bases to adopt Watson-Crick pairs
permits bases on same strand to stack
DNA in form of Chromosome -the bigger the x-some, the more protein associated to it
-phosphate group on backbone interact ionically to histone to form nucleosomes
-contain other proteins so called non-histone x-somal protein
What is a DNA hairpin structure? palindrome sequences can form hairpins (single strand)
What is a second messenger? an intracellular ion or molecule that acts as a signal for an extracellular event such as ligand binding to a cell-surface receptor
second messengers are often nucleotides
What consequence does the hydrogen-bonding between base pairs have on DNA structure? with bases H-bonding to one another, the sugar-phosphate backbone forms a helical structure outside
On switch for cAMP adenylate cyclase ATP --> cAMP + 2 Pi
DNA stores genetic info while RNA transcript and translates it, except? when regarding virus. some virus caries their genetic code in their RNA
How much energy is released by the hydrolysis of phosphodiester bonds? hydrolysis of phosphodiester bonds releases ≈30/kJ per bond of energy
Result when you grow cells in 15N (heavy DNA), isolate DNA, and centrifuge DNA one band low in tube
where does exo a phosphodiesterase cleaves? Cleavage on the a side (3' end), leaves the phosphate attached to the 5'-position of the adjacent nucleotide
What is the tertiary structure of nucleic acids? tertiary structure is the folding of nucleic acid into chromatins or nucleoids
What are the main differences between DNA and RNA? DNA - double stranded with Thymine as base and deoxyribose as sugar
RNA - single stranded with Uracil as base and ribose as sugar
What types of structure is RNA capable of having? RNA forms complex structures of SINGLE STRAND nucleic acid
single strand can form a helix, stabilized by base-pairing interactions but self-complemetary regions will form even more complex structures (hairpins, etc.)
When RNA does take on some rare double stranded structures what is the most common form? these double stranded RNA regions more readily adopt A-form (as opposed to DNA which adopts B-form)
What is the general trend of Tm based on the energies required to break H-bonds between base pairs? as the GC content of DNA increases, the Tm decreases as this base pair is more difficult to break