What will the complete hydrolysis of nucleic acids yield?
The individual components; nucleobases, pentose sugar, and phosphate
How many H-bonds are between G&C and between A&T/U?
There are three hydrogen bonds between G&C and two hydrogen bonds between A&T/U
What stabilizes the double helix?
Combination of hydrophobic forces and van der Waals interactions; H-bonds between bases from opposite strands
What is hybridization?
It is a technique based on the association of complementary strands; based on the capacity of complementary strands to anneal in which one of the strands is labeled with radiotracer or a fluorescence marker
How many forms of DNA are there and what are they called?
B DNA, A DNA, and Z DNA; B DNA is the physiological form we think of in regards to DNA, it has is right handed and there is one helical turn ~ every 10 bps
What is the difference between negative and positive supercoiling?
Negative twists in the opposite direction of the double-helix, and unwinds DNA; positive twists in the same direction as the double helix and
What type of DNA can undergo supercoiling?
Only covalently closed circular DNA or ends-constrained linear DNA can undergo supercoiling
Negative supercoiling of bacterial DNA
Gyrase negatively supercoils bacterial DNA; results in transient double stranded breaks; supercoiling is ATP-dependent and it aids in DNA packing, replication, and transcription; this mechanism is the target of anti-bacterial drugs (ciprofloxacin and novobiocin)
What are the two epigenetic modifications which alter chromatin structure?
Methylation of C residues in –CpG- and histone modification
What does methylation of –CpG- lead to?
Generally leads to chromatin compaction and gene silencing; methylation of Cs in CpG islands results in long-term silencing of a gene; inactive X csome and other imprinted genes are heavily methylated
What are CpG islands?
Regions of DNA with a high density of CpG dimers; these are found in the regulatory regions of most human genes
What does histone modification lead to?
This is a post translational modification of histone tails, and the result of this modification depends on which histone is modified; acetylation generally leads to open chromatin structure and activation of genes
How are histones acetylated and deacyetylated?
A gene activator recruits histone acetyltransferase to acetulate a histone; a gene repressor recruits histone deacetylase to deactylates the histone
Structure of RNA
Mostly single stranded, but the strands to loop back to form intra-strand base-pairing (this defines the structure of RNA); where the RNA loops back and is paired, the strands are anti-parallel
Transfer RNA (tRNA)
75-85 bases long; contain bases like pseudouridin and ribothymidine; there is one tRNA for every AA; serves as an adaptor molecule during protein synthesis; forms a two dimensional “clover leaf” structure; it is compacted to a highly folded L-shaped conformation; one end of the L has an anticodon loop with the other end having an AA binding site attached to the 2’C or 3’C of the sugar; the 3’ end has the sequence CCA
AN AA attached to a tRNA molecule
What rRNA sizes are found in prokaryotes?
23S (catalyzes the peptide bond formation), 16S (helps identify the first codon during translation), and 5S
What rRNA sizes are found in eukaryotes?
28S, 18S, 5.8S, and 5S
Does rRNA base bair?
Yes, it has considerable intra-strand base pairing
Messenger RNA (mRNA)
Least abundant, with a short half-life, this RNA has very little intra-strand base pairing; its primary sequence encodes proteins; it has a 5’ cap (7-methylguanosine triphosphate) and a poly(A) tail at the 3’ end; prokaryotic mRNA does not have a cap and tail
What additional functional RNAs are found in eukaryotes?
hnRNA, snRNA, scRNA, lncRNA, miRNA, and siRNA
mRNA precursors; has 5’cap and poly A tail
There are 90; several hundred nucleotides long; U-rich, involved in the maturation of pre-mRNA
Associated with proteins involved in the recognition of signal peptides on proteins
Over 200 bases; some are capped, polyA tailed, spliced; Xist silences one of the X csomes
Single stranded; 19-25 nucleotides long; may target up to hundreds of
mRNAs; non-coding, purely for regulatory purposes important for post-transcriptional gene silencing, affects a wide variety of cellular functions; role in cancer, viral infections, and wound healing; inhibits
translation of mRNA
Double stranded; 21-22 nt; knock down specific genes; regulates the gene that expresses it; cleaves mRNA; acts as gene-silencing guardians in plants and animals that do not have antibody or cell-mediated immunity
Transition temperature Tm
Temperature at which 50% of the helix is denatured
An increase in absorbace at 260 nm, associated with denaturation; this
is the wavelength at which nucleobases absorb light