Lecture 5 - Nucleotides and Nucleic Acids Flashcards
What are the functions of nucleotides? (7)
- energy metabolism (ATP)
- enzyme cofactors (NAD+)
- signal transduction (AMP)
- storage of genetic information (DNA)
- Transmission of genetic information (mRNA)
- catalysis (ribozymes)
- protein synthesis (tRNA and rRNA)
What is a nucleotide?
a nitrogenous base with a pentose and phosphate moiety attached to it
What is a nucleoside?
a nitrogenous base with a pentose attached (no phosphate)
What is a base?
a nitrogenous base attached
What does a prime(‘) indicate?
it indicates that they are associated with the sugar referring to the carbons on that sugar molecule
When is a molecule ribose?
when there is a hydroxyl group associated on the two prime (OH)
When is a molecule deoxyribose?
when the 2’ prime OH group is not there, instead there is a hydrogen atom
A 5’ hydroxyl occurs on a?
nucleoside
A 5’ phosphate occurs on a ?
nucleotide
What is the charge of a phosphate group at neutral pH?
negative
Nucleic acids are built using what?
5’-triphosphates
how many phosphate moieties does nucleic acids contain per nucleotide?
one
If the OH goes to the right, what is its configuration?
D
What are the two forms that pentose exist in solution?
- linear
2. cyclic
What are the characteristics of Nucleobases? (4)
- derive from pyrimidine or purine
- nitrogen containing heteroaromatic molecules
- planar or almost planar structures
- absorb UV light around 250- 270 nm
In pyrimidine bases, cytosine is found only in?
both RNA and DNA
In pyrimidine bases, thymine is found only in?
DNA
In pyrimidine bases, uracil is found only in?
RNA
In purine bases, adenine and guanine are found in?
both rna and dna
What other name is the first carbon prime referred to as?
anomeric
In nucleosides and nucleotides, the pentose ring is attached to the base via an?
N-glycosidic bond
The bond in a B-N-Glycosidic molecule is fomed to: (2)
- to position N1 in pyrimidines
2. to position N9 in purines
anti conformation is found in?
normal B-DNA
5-methyldeoxycytidylate is common in ___ and found in ___
eukaryotes; bacteria
How does a epigenetic marker work in prokaryotes?
it is a way to mark your own DNA so that cells can degrade foreign DNA
What is epigenetic marker: negative regulation in eukaryotes?
ways to mark which genes should be active
Pseudouridine is found widely in?
tRNA and rRNA
In polynucleotides, covalent bonds are formed via?
phosphodiester linkages with a negatively charged backbone
DNA backbone is ___ while rna backbone is ____
stable; unstable (mrna will degrade in a few hours)
Why is RNA less stable than DNA?
the presence of the 2’ hydroxyl group is the difference between the two
What is RNase?
an enzyme that will catalyze the hydrolysis, do if it’s hydrolyzing then RNase can activate the water molecule and nail the nucleophile
characteristics of the Watson Crick Model of B-DNA
- double stranded dna structure
- right handed helix
- 10.5 base pairs per turn
- minor groove = 3.4 A
- major groove = 36 A
How does your protein read the nucleotide sequence of your DNA?
by slipping into the major groove; the protein will hydrogen bond to the sequence that it is suppose to read; the kd will dictate how well it binds, the greater the affinity the more it’s going to bind
Complementarity of DNA strands: (3)
- two chains differ in sequence
- two chains are complementary
- two chains run anti-parallel
what is polycistronic?
coding for one or more protein
what is messenger RNA?
it is a code carrier for the sequence of proteins
mRNA is synthesized during?
DNA template
mRNA contains: (3)
- ribose instead of deoxyribose
- uracil instead of thymine
- single strand
what is tRNA?
matching amino acids with the mRNA code
