Chapter 3 and 24: Nucleic struc and org Flashcards
Base Tautomeric forms structures
GO OVER S. 2
Nucleosides makeup (specific with what type of bond)
Nitrogenous base + Sugar
-D-ribose or deoxy-D-ribose sugar that is connected to a base by a beta-N-glycosidic bond
Nucleotides
Nucleoside + Phosphate
-nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, at the 3’ or 5’ OH
*5’ OH is the default
3’-5’-Cyclic adenosine monophosphate (cyclic adenosine monophosphate, cAMP) derivation and how it is used?
-derived from ATP
-cAMP used in intracellular signal transduction as a secondary messenger
DNA struc. and bases
-deoxyribose
-A,G,C,T
-ex: deoxy= deoxyadenosine–> dAMP–>dADP–>dATP
RNA struc and bases
-ribose
-A,G,C,U (sometimes T)
-ex: Adenine–>Adenosine–>AMP–>ADP–>ATP
Modular struc config struc
know slide 4
Zidovudine
-used in medicine:
nucleoside analog reverse transcriptase inhibitor (NRTI) used to treat HIV
minor bases (RNA vs. DNA and their role)
-RNA (tRNA) contains minor bases
-In DNA minor bases are methylated forms of the major bases
*have roles in regulation or in protecting genetic information
Inosine
-type of Xanthines that is a minor base
-found in tRNAs
-essential for wobble base pairs (anticodon)
DNA and RNA simple def
-known as polynucleotides= nucleotides joined by phosphodiester linkages
-RNA= ribonucleic acids
-DNA=deoxyribonucleic acid
Primary structure seq of DNA
read from the 5’ to 3’ end
what is RNA susceptible to?
Base catalyzed hydrolysis bc it has a 2’ OH
-why DNA is more stable
Erwin Chargaff
found chargaff’s rule
-A=T
-G=C (stronger)
Watson and Crick
solved secondary structure of DNA by using Franklin’s data
-found the double helix
-Crick: crystallographer who knew it was a helix
-used chargaff rule
Rosalind Franklin
-got the X-ray fiber diffraction data
*helped watson and crick with solving DNA struc
Central Dogma
- Replication using DNA polymerase
- Transcription (DNA->RNA) using RNA polymerase
- Translation (RNA->Protein) using ribosomes
- Protein
DNA structure total (facts)
-right/left handed helix
-bases are perpendicular to helix
-bases: minor and major grooves
-phosphate backbones are on the outside
-anti-parallel chains
-bases pairs per helical turn: 10
-Pitch= 34A
-Helix rise per base pair = 3.4A
-Diameter: 20A
-glycosidic bond formation: anti
Nucleotide sugar conformations in DNA/RNA
Syn-adenosine
anti-Adenosine
*sugar is anti to the base
Differentiate between A-DNA, B-DNA, and Z-DNA
A-DNA
-right handed helix
-Major groove: narrow and deep
-Minor groove: wide and shallow
B-DNA
-right handed helix
-Major groove: wide and deep
-minor groove: narrow and deep
Z-DNA
-left handed helix
-Major groove: flat
-minor groove: narrow and deep
RNA-RNA/RNA-DNA hybrids assume which sturcture
A DNA
Z-DNA occurs in what and is favored when?
-occurs in alternating purine-pyrimadine tracts
-favored in high salt concentrations
Telomeres
the ends of linear chromosomes
Tetraplex or Quadruplex DNA have what kind of roles?
roles in transcription, telomere maintenance, DNA recombination etc….
RNA structure
-mostly single-stranded
-has a wound back double helical regions that assume A type helix
Ex: stem loop, hairpin
Secondary and Tertiary structure of tRNA
-2nd: cloverleaf
-3rd: L or banana
Topoisomerases general
relax (or make) supercoils in DNA by causing a transient nick that is resealed
Topoisomerases: Type I
relax (some make) supercoils by breaking only 1 strand
-ssDNA break
Topoisomerases: Type II
relax or make supercoils by breaking both strands
-dsDNA break
Topoisomerases inhibitor: Quinolones like Cipro
-binds two bacterial type 2 topoisomerase
-DNA gyrase and topoisomerase IV needed for replication
-causes inhibition of DNA replication and cell death
*freezes enzyme in this step when it makes DS break- doesnt let enzyme reseal DNA
Human: number of base pairs
3,200,000
3.2 billion
size relation btwn DNA and bacteria
bacteria: 2 uM
DNA: 1,600 uM
Prokaryotic DNA: packaging
-supercoiled circular DNA is bound to small, basic proteins to give bacterial chromosomes in the nucleoid
Bacterial Plasminds
sep. small circular molecules that carry genes for their own replication and often code for beneficial enzyme degradation (resistance)
Eukaryotic DNA packaging
-package DNA as chromatin fibers at normal stage of cell cycle but into chromosomes when cells are about to divide
how long is human DNA?
1 m
How is DNA coiled
coiled around a histone octamer which is also called a nucelosome
-H2A, H2B, H3, H4
Nucelosomes in relation to DNA
-beads on a string under microscope
-has 1.8 turns of DNA (146 bp) wound around nucleosome
Histones
-small proteins rich in the basic amino acids Lysine and Arginine
-positively charged
Histone: H1
-Not part of nucleosome
-bound to the DNA in btwn the nucleosome
Mitochondrial (mtDNA) and Chloroplast DNA (ctDNA)
-circular DNA
-devoid of histones
-replicate on their own
*used for forensic analysis
DNA damage
-UV-irradiation
-Thymine dimers
-Alkylation
-HNO2
Alkylation
causes DNA mismatch mutations that can lead to cancer
HNO2
-from food cured with NaNO2
-causes DNA mismatch mutations that led to cancer
