Unit 3 Structure of Nucleic Acids

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1

Nucleic Acids:

Two Types;Function

Types: Deoxyribonucleic acids (DNA) & Ribonucleic acids (RNA)

Function: Storage and expression of genetic information

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Central Dogma of Molecular Biology

DNA -> RNA -> Protein

Replication, Transcription, Translation

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English Translation of "Genome"

I become, I am born, to come into being

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Organization of Genome: Prokaryote

Prokaryote: DNA protein complex in nucleoid
Viruses: DNA or RNA; Lack of complete system for rep, transc. transl.
Plasmids: small circular DNA; replicate autonomously outside host genome; used in genetic engineering

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Organization of Genome: Eukaryote

DNA w/ histone= Chromatin; Diffuse= euchromatin; Condense= heterochromatin
6 X 10^9 base pairs in humans; 46 Chromosomes (Human)

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Structure of DNA

Phosphodiester bond: 3'C and 5'C; Complementary base pairing with hydrogen bonds: CG 3H bonds & AT 2H bonds

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Forms of DNA

A- loose, dehydrated DNA, DNA-RNA hybrid, enzyme-DNA complex; B- most common standard; Z- initiation of transcription and methylation: Z-DNA binding proteins involved in regulation of transcription

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Major Groove and Minor Groove

Used for binding of: regulatory proteins (transcription factors), antibiotics, & anticancer drugs

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Properties of DNA

DNA helix separated by alkali and heat (denaturation or melting); alkali also breaks phosphodiester bonds in RNA, but not DNA;

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Tm

Temperature at which 50% of DNA is melted. High GC= higher Tm; SLOW temp decrease = reformation of dsDNA (renaturation or hybridization)

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DNA Hybridization

Detection of specific sequences techniques: fluorescent in situ hybridization (FISH) & southern (DNA) and northern (RNA) blot

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PCR

used to amplify specific DNA sequences

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Genomic DNA Compaction: Prokaryotes

DNA supercoiled and attached to RNA-protein core= nucleoid;

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Genomic DNA Compaction: Eukaryotes

DNA much larger than prokaryotes and needs to fit into nucleus- binds to histones (basic proteins, five major classes: H2A, H2B, H3, H4, and H1) DNA-histone complex: chromatin

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Nucleosome Core

8 histone molecules, 140 bp DNA wrapped around coire; linker DNA complexed w/ histone H1; tubular coil= solenoid (30nm fiber) Other proteins bound: enzymes & regulators; all essential for controlling transcription

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Nuclear Scaffold Proteins

30nm fiber organized into loops and anchored to nuclear scoffold protein to form chromatid, which is bound to another sister chromatid by a centromere to form a chromosome.

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Chromosome Territories

each chromosome occupies distinct territory in nucleus with preferred nuclear locations- chromosome domain

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HIstone Acetylation and Transcription

Histone Acetylltransferase (HAT) acetylates histones reducing positive charge and creates open chromatin; different enzymes methylate H3 on Lys4, 9, 27, & 79- F(x) silencing and activating

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Gene, Genetic Locus, & Allele

Gene: basic unit of heredity; Genetic Locus: position of gene on chromosome; Allele: alternative version of gene; Humans- 25k genes, 1.5% of genome protein-coding exons

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Karyotyping

determines diploid number of chromosomes; chromosomes arranged into karyotype or karyogram- used to determine sex and spotting abnormalities.

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Chromosome Abnormalities

Two basic groups: numerical and structural anomalies

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Turner Syndrome

Single X chromosome in females- 1:2.5k births, infertile, cardiovascular and kidney problems, low estrogen leads to osteoporosis

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Klinefelter Syndrome

XXY male; 1:500 males; infertile, gynecomastia (large mammary glands in males), high incidence of germ cell tumor and male breast cancer

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Edwards Syndrome

trisomy of chomosome 18; 1:3k pregnancies & 1:6k births (more births than pregnancies?), kidney malformation and structural heart defects, protruding intestines out of body & developmental delays

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Down Syndrome

trisomy of chromosome 21; 1:0.8-1k births

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Patau Syndrome

trisomy of chromosome 13; 1:12k births; microcephaly, heart and kidney defects, & abnormal genitalia

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Types of RNA

mRNA, rRNA, tRNA; RNAse P cleaves extra sequence of RNA on tRNA; Peptidyl transferase- activity of ribosome

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mRNA

5% of RNA; most heterogeneous type of RNA: Cap on 5' end initiates translation (added during transcription), Coding region translated, Poly-A tail 3' end stabilizes mRNA (added after transcription)

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rRNA

70% of RNA; + mRNA for ribosomal proteins= 90%; synthesis of rRNA & assembly of ribosomes in nucleolus

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Ribosomes

Prokaryotic: three types of rRNA and less protein

Eukaryotic: four types of rRNA and more proteins

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Structure of tRNA

~80 nucleotides; cloverleaf formed by pairing antiparallel manner; 20 diff tRNAs- one for each AA; 10-20% nucleotides in tRNA modified; AA attached to 3' end; Anticodon interacts w/ codon on mRNA; provides proofreading during translation

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Other Types of RNA

Primers for replication of DNA; snRNA- part of snRNPs splices RNA; miRNA- 20-24 nucleotide non-coding from endogenous- repress protein biosynthesis preventing ribosome binding to mRNA

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Other Types of RNA cont.

lncRNA- >200 bp, epigenetic mods of DNA eg: Xist RNA- inactivates X chromosome in vertebrates; lincRNAs >200 bp eg: scaffold DNA-chromatin complexes

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Inhibitors of DNA Synthesis

Nucleotide analogs slow division and growth: AZT- replace hydroxyl group by azido group (reverse transcriptase high affinity); ddl- remove OH from deoxyribose; arabinose- convert deoxyribose to another sugar

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Base Analogs

5-FU inhibits synth of thymine nucleotides by thymidylate synthase inhibition which converts dUMP to dTMP; 5-FU -> F-dUMP which is the actual inhibitor