Nucleic Acids: Carriers of Biological Information Flashcards
What is the central dogma?
DNA–>RNA–>protein
Number of chromosomes (total and of each kind)
46 total
44 autosomes (22 pairs)
2 sex chromosomes (1 pair)
Classes of RNA species in human cells
(3)
Structural RNAs
Regulatory RNAs
Information containing RNAs
Structural RNAs
rRNA
tRNA
snRNA
snoRNA
Information containing RNAs
mRNA
Regulatory RNA
miRNA
siRNA
Purines
Adenine and Guanine
two rings: imidazole and pyrimidine rings
Pyrimidines
Cytosine, Uracil, Thymine
one ring
Nucleoside
sugar (ribose or deoxyribose) + base (purine or pyrimidine)
Ex: adenosine, guanosine, thymidine, cytosine, uridine
Nucleotide
base+sugar+phosphate group
Deoxyribonucleotides
dAMP, dGMP, dTMP, dCMP
Ribonucleotides
AMP, GMP, UMP, CMP
Relative solubility of 5 components of nucleotides
pyrimidines>purines
nucleotides>nucleosides>bases
*Gout and Lesch-Nyhan disease: build of of purines of low solubility in tissues
Nucleotide and deoxynucleotide residues in RNA and DNA are joined by _______ into strands with _______ polarity
phosphodiester linkages
5’–3’ polarity
Nucleoside Di and Tri phosphates
base (purine/pyrimidine)+ sugar(ribose/deoxyribose)+ 2-3 phosphates (ADP, ATP, GDP, GTP, etc.)
Phosphodiester bond
3’ OH attacks 5’ alpha phosphate; Leads to two alcohols esterically bound to molec of phosphoric acid (C-O-P-O-C)
Chargaff’s Rule
DNA from any cell should have 1:1 ratio of purine and pyrimidine bases
%G=%C
%A=%T
Avery, McCloud and McCarty
Experiment:
Live encapsulated virulent bacteria to mouse–>dies
Live nonencapsulated nonvirulent bacteria to mouse–>lives
Heat virulent bacteria (kill/denature)–>mouse lives
Denatured fatal bacteria into live nonvirulent bacteria–>mouse dies
Live nonvirulent bacteria mixed w/ DNA from virulent–>mouse dies
protein doesn’t transfer genetic info, DNA does
Hershey and Chase
Bacteriaphage: radioactive label for DNA (exp 1) radio label for protein coat (exp 2)
Label showed in new bacteriaphages ONLY in exp 1–> DNA transfers genetic material, not protein
Franklin and Wilkins
XR diffraction of DNA showing helical structure, 10 layer lines, 3.4 nm repeat
B form DNA:
two strands intertwined in _____ helix
right handed
DNA backbone are ____ to each other
anti-parallel
5’–>3’ and 3’–>5’
Where is the sugar phosphate backbone? bases?
on outside of helix
stacked on inside
How many steps for DNA to get back to same position?
10
Major groove and minor groove lengths
Major: 22 A (proteins like tfs usually make contact w/ bases in major groove, easier to access)
Minor: 12 A
What are the two factors important to the stability of the DNA (overcome negative charge on each phosphate)?
- ) Hydrogen bonds (A:T 2 H bonds, C:G 3 H bonds)
2. ) Stacking energies (hydrophobic interactions)
Factors affecting Tm.
- Salt Concentration
- pH extremes
- Increases in DNA chain length (increase Tm)
- Increasing GC content (increase Tm, 3 H bonds for GC)
Why does salt concentration affect Tm?
High salt, higher Tm because positive charges stabilize negative charges on phosphate groups.
Why do extremes of pH affect Tm?
Extreme pH affects the ionization states of the groups on the bases which provide/accept H bonds
Major covalent modification of human DNA?
Covalent methylation of cytosine at 5’ C in CpG sequences.
Add methyl group, repress transcription, silence gene.
Methylation of adenine
In bacteria like E. coli, methylation of adenine helps DNA repair enzymes identify older strands of DNA, which are used as a reference for repairing damage during DNA replication.
De-amination of bases
Exposure to nitrous acid precursors can cause loss of amine group from base. 5mC:G can be changed to T:G w/ deamination. Leads to T:G mismatch. Mismatch can be fixed, but T has 50% chance of remaining. MAJOR CAUSE OF MUTATION.
Depurination
Remove purine (base) from sugar (break beta glycosyl bond linkage). After depurination, backbone is sensitive to breakage.
Oxidative damage
-OH (reactive oxygen free radical) from mitochondria can damage DNA, -OH groups on bases disrupt structure
UV light damage
UV light can cause adjacent thymine to covalently bond to one another. (kink in DNA)
Base alkylation and examples
Reaction of alkylating agents forms large covalent adducts to DNA, can cause issues w/ replication and transcription.
Ex: Carcinogens, benzene, dimethylnitrosamine, nitrogen mustard, dimethylsulfate, [Cisplatin–>cancer drug, similar mech]
Ex of intercalation
doxorubicin (chemotherapeutic agent), actinomycin D (natural)
What do etoposide and camptothecin do?
chemotherapeutics that target topoisomerases which are needed to relax DNA supercoiling. (Drugs interfere, thus leaving breaks in DNA that can’t be repaired)
Linear vs circular DNA locations
linear: in nuclear chromosome
circular: mitochondria only
Underwound DNA produces _______
negative supercoils, decreased twist
Overwound DNA produces_____
positive supercoils, increased twist
What do topoisomerases do?
They “relax” supercoiling by breaking the DNA backbone.
Needed for DNA replication.
DNA polymerization
DNA is added 5’ to 3’. 3’ OH nuclophilic attack of 5’ alpha phosphate.
Nucleoside analogues
Used to be antiviral drugs that halt viral DNA replication.
On 3’ C, there is not and OH group, there is N=N=N (Azide) or Hydrogen. No nucleophilic attack of phosphate, so replication stops. (AZT, ddl–>HIV treatment)
DNA and RNA similarities
2 pyrimidines, 2 purines
5C sugar, phosphate group, base
Sugar-phosphate backbone
Adenine, Guanine, Cytosine
DNA and RNA Differences
Uracil vs. Thymine
Single strand vs. Double strand
Ribose vs Deoxyribose sugar
DNA more stable than RNA
DNA codes for RNA, RNA codes for protein
RNA has enzymatic function too, DNA is info storage
Diff protein interactions (RNA pol vs DNA pol)
RNA has greater flexibility, structural capacity almost to protein level
Why is RNA unstable?
3’ OH can act as a nucleophile and attack nearby phosphate, thereby destabilizing the backbone. (RNA more susceptible to hydrolysis.)
Puromycin
An antibiotic that mimics the 3’ acceptor end of tRNA that is charged with an aa. It can bind in the ribosome and covalently attach to growing poplypeptide chain, thus stopping translation. Steptomyces makes it, and also has enzyme to stop it.
RNA hairpin folds using ______ connections
AU, GU, GC base pairs
Information containing RNAs do what?
mRNA: translated into proteins
Structural RNAs do what?
tRNA, rRNA, snRNA (small nuclear RNA).
tRNA and rRNA form machinery to convert mRNA into protein (rRNA provides peptidyl transferase activity) (tRNA transfers amino acid to growing chain at ribosomal site of protein synth)
snRNA splices mRNA from longer initial forms
rRNA is a ribozyme (has enzymatic activity)
Regulatory RNAs do what?
use base-pairing and interaction w/ proteins to up or down regulate cellular processes like transcrip and translation (microRNAs, small interfering RNAs)
