Download Composition and structure of DNA and RNA and differences

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Composition and structure of DNA and RNA and differences between two
o DNA
 DNA structure:
 Base –purine (A, G) or pyrimidine (C, T)
 Sugar deoxyribose (lacks –OH at C2)
 Phosphate—PO4 forms “backbone”
 Nucleoside: purine/pyrimidie base + sugar linked by N-glycosidic bond
 Nucleotide: purine/pyrimidie base + sugar + PO4 (ester linkage at 5’ –OH
group)
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DNA base pairing
o A-T, 2H bond
o C-G, 3H bond
DNA polarity
o 5’ phosphate to 3’ free hydroxyl
 3’ hydroxyl where new nucleotide can be added via
phosphodiester bond
Double helix is coiled around axis of symmetry
Paired in anitparrallel fashion
Major and minor grooves
o Major groove major site of protein binding also aided by negative
charge
o Certain anticancer drugs such as dactinomycin (atinomycin D), exert
a cytotoxic effect by intercalating into the narrow grove and
interfering with DNA synthesis.
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RNA structure
o Different from DNA
 Major difference is hydroxyl of 2’ sugar
 Minor difference use of Uracil instead of thymine
o Structure:
 RNA chains are usually single-stranded and lack continuous
helical structure
 RNA can have considerable secondary structure and tertiary
structure because base pairs can form in regions where the
strand loops back on itself
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DNA damage
o Both heat and alkali (base) cause the two strands of the double helix to
separate
o Alkali (base) will not break the phosphodiester bonds of DNA, but it
will cleave phosphodiester bonds of RNA
o Heat alone converts double-stranded DNA to single-stranded DNA
o Separation of DNA strands is called “melting” and the temperature at
which 50% of the DNA is separated is call the Tm. DNA with a high
content of GC= higher Tm
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Hybridization of DNA/RNA
o Seen during transcription process
o mRNA can also inhibit transcription through binding
The Central Dogma
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Forms of DNA
o The B form is a right-handed helix with ten residues per 360o turn of the helix,
and with the planes of the bases perpendicular to the helical axis. Chromosomal
DNA is thought to consist primarily of B DNA
o The A form is a right-handed helix but there are 11 bases per turn and the planes
of the base pairs are tilted 20o away from the perpendicular to the helical axis.
The conformation found in DNA-RNA hybrids is probably close to the A form.
o Z-DNA is a left-handed helix that contains about 12 bases per turn. The
deoxyribose-phosphate backbone zigzags (hence the name Z-DNA). Transitions
between the B and the Z helical forms of DNA may have a role in regulating gene
expression.
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Chromosome structure
o Histones:
 Protein core made of 2 H2A, H2B, H3 and H4 along with H1 linker
o Centromeres:
 Spindle fibers attach during mitosis and meiosis here
 If you lack centromere chromosome can be lost during mitosis
o Telomeres
 Protect ends from degradation or fusion
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Structure of chromosomes (role of histones, nucleosomes, etc)
o Linear double strand helix> supercoil> chromatin-DNA helix + histones=
nucleosome> solenoids (loops)> chromosome > genome
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Forms and functions of RNA (mRNA, rRNA, tRNA)
miRNAs
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role in normal cell regulation activity, some associated with
cancer
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Eukaryotic tRNA
o 20 different tRNAs
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Eukaryotic rRNA
o Riobosome
o Cytoplasmic ribosomes in eukaryotes 4 types:18S, 28S, 5S and
5.8S >> 80S
 Prokaryotic ribosomes contain three types of rRNA
molecules with sedimentation coefficients of 16, 23, and 5S
(dependent on density and shape of complex) >> 70 S
 Mitochondria >> 70S properties, 55S
Identify structure and function of genes
o Eukaryotic mRNA consists of
 A leader sequence at the 5’-end
 A trailer sequence at the 3’-end
 The leader sequence begins with a guanosine cap structure at its 5’ end
(added after transcription)
 The coding region begins with the trinucleotide start signal of translation
or AUG (initiating methionine)
 Translation ends via a termination signal.
 The trailer sequence terminates at its 3’-end with a poly (A) tail up to 200
nucleotides in length (added after transcription)
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Identify the life cycle of a retrovirus
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Know the clinical uses of azidthymidine, doxorubicin and 5-FU—site and mechanism of
action
o Erythromycin (a macrolide antibiotic)
 acts by inhibition of protein synthesis in susceptible organisms
 reversibly binds to 50 S ribosomal subunits (prokaryotes)
 causing inhibition of translocation of aminoacyl transfer-RNA (stops
protein synthesis
o 5-fluorouracil (5-FU)
 pyrimidine base similar in structure to uracil (RNA) and thymidine (DNA)
 inhibits synthesis of thymidine nucleotides used for DNA replication
 thymidylate synthase (TS) converts dUMPdTMP
 the active form of 5-FU converts to5-FdUMP that irreversibly binds TS
 used in chemotherapy to “knockdown” DNA synthesis----cell
replication
o Doxorubin: DNA intercalator
 Anthracycline antibiotic: works by intercalating into the DNA interior
and disrupting the helix---used as a chemotherapy agent; disrupts DNA
replicationcell replication
o Azidothymidine: anti-retroviral
 AZT is the first drug approved for treatment of AIDS and HIV
infection
 A reverse transcriptase inhibitor (enzyme used by HIV to make a copy of
it’s RNA genome
 Also inhibits DNA polymerase γ (may produce the side effects)
 Does not destroy infection
 Has adverse side effects
 Frequently used in combination therapy