Exam 4: Nucleic Acids Flashcards Preview

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Flashcards in Exam 4: Nucleic Acids Deck (50):
1

Noncoding DNA sequences

DNA that does not code for proteins (Spacer sequences, Introns, Genes encoding nonprotein-coding RNAs, Repetitious DNA)

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Spacer sequences

DNA sequences that separate genes

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Introns

Noncoding sequences within gene - spliced out of primary RNA and transcribed into mRNA or protein

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Repetitious DNA sequences

Satellite DNA (repeats of relatively short sequences, give DNA weight, mostly confined to centromere and telomere), interspersed repeats (dispersed throughout the genome, many copies of transposons and retrotransposons)
half of DNA - noncoding sequences

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Exons

sequences of DNA translated into protein

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Gene families

genes that have similar nucleotide sequence and encode similar proteins
come from gene duplication that accumulates mutations over time
can be clustered at one chromosomal locus or dispersed throughout the genome

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pseudogene

Gene family duplicate that was inactivated by mutation

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Chromatin

complex of DNA and protein (1/3 DNA, 2/3 protein)
DNA wrapped around histones, then associated to form a fiber, then fiber forms wide loop domains
During condensation for cell division looped domains attach to protein scaffold to form wide fibers

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Nucleosomes

DNA wrapped around histone proteins
146 bp wrapped around two of each of 4 histones (H2A, H2B, H3, H4)
5th histone (H1) attaches and seals structure

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Chromosomes

DNA organized into large linear molecules
in division each chromosome consists of two identical DNA strands - chromatids - attached to each other at centromeres

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Chromatid

identical DNA strands attached to form chromosome during G2 & M phases of cell cycle

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Telomeres

special sequences at ends of chromatids
DNA forms a loop to protect free end from degradation

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Haploid

cells containing one copy of each chromosome
In humans only egg and sperm are haploid

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Diploid

cells containing a maternal and paternal copy of each chromosome - homologous chromosomes

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Mitochondrial genome

different from nuclear genome
Circular, multiple copies per organelle
not extensively associated with proteins

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Nuclear envelope regulates

Access of proteins to DNA;
Separation of translation and transcription - allows for post-transcriptional modification of RNA

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Heterochromatin

intensively stained on electron micrograph - complexed with proteins, highly condensed, and transcriptionally inactive
Located on periphery of nucleus

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Euchromatin

translucent on electron micrograph - transcriptionally active, decondensed DNA, not associated with as much protein

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Nucleolus

large, intensely stained area on electron micrograph - internal structure, contains genes encoding ribosomal RNA
Actively transcribed

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nuclear matrix

protein scaffold that attaches to chromosomes

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Chromosomal territory

each chromosome occupies a distinct territory of nucleus

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Interchromosomal domains

separate chromosomal territories

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Nuclear envelope

double-membrane, contiguous with endoplasmic reticulum
contains nuclear pores - only way to enter nucleus

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Nuclear pore

regulate traffic between nucleus ad cytoplasm
Energy-dependent to transfer proteins into nucleus

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3 main types of large molecues that must be actively and selectively transported into/out of nucleus

mRNA, proteins, ribosomal subunits

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Ran

small GTP binding protein that mediates import and export from nucleus

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Import of protein into nucleus requires

Protein associated with importin, inside nucleus importin associates with Ran-GTP an releases protein, importin/Ran complex transported out of nucleus, Ran-bound GTP hydrolyzed -release of importin, Ran-GDP reenters nucleus and converted back to Ran-GTP

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Export of protein from nucleus requires

protein to associate with exportin and Ran-GTP, outside nucleus, Ran-GTP is hydrolyzed to Ran-GDP and complex dissociates, Exportin and Ran-GDP transported back into nucleus, and Ran-GDP converted to Ran-GTP

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DNA polymerases

enzymes that synthesize DNA
Alpha, Beta, Delta, Epsilon function in replication and/or repair of nuclear DNA
Gamma functions in mitochondrial DNA replication

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DNA polymerases share these properties

enzymes template-directed
primer required (can't initiate DNA synthesis)
synthesize DNA only in the 5' to 3' direction
dATP, dGTP, dCTP, and dTTP are nucleotide donors for DNA synthesis

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Primase

primer to initiate DNA replication, made of RNA
degraded by exonuclease - not in final DNA product

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origin recognition complex (ORC)

binding proteins that mark origins of replication
during S phase, activation of proteins associated with ORC allows initiation of replication - then inactivated, replication can't be re-initiated

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DNA helicases

unwind DNA double helix using free energy of ATP hydrolysis
Start at origins of replication

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Single-stranded binding proteins

bind to exposed single strands of DNA to prevent from re-associating

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Topoisomerases

relieve supercoiling of adjacent regions of unwound DNA for replication to progress
Nick & re-ligate DNA strands - allow supercoils to unwind
Type I: cut backbone of one strand of DNA & re-ligate
Type II: manipulate two double helices at same time

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DNA polymerase alpha

synthesizes short RNA primer - primase activity

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Sliding clamp accessory proteins

adjacent to primer on DNA - allow enzyme to synthesize more DNA before falling off template

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DNA polymerase epsilon

synthesizes DNA on leading strand (toward growing replication fork) - synthesized continuously in 5' to 3' direction

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DNA polymerase delta

synthesizes DNA on lagging strand (away from replication fork) - synthesized discontinuously in 3' to 5' direction (even though actual synthesis still occurs in 5' to 3' directions, just smaller fragments - Okazaki fragment)
Fills in gaps after RNA primers removed

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DNA ligase

joins together Okazaki fragments - requires ATP

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Telomerase

contains an RNA molecule that is complementary to repeat sequence of telomere - acts as a template (TTAGGG) for extension of 3' end of DNA so ends of chromosomes don't get shortened

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Purine

Adenine and Guanine

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Pyrimidine

Thymine (Uracil in RNA) and Cytosine

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Guanine-cytosine forms

3 hydrogen bonds

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Adenine-thymine forms

2 hydrogen bonds

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Most protein-DNA interactions take place via

major groove (portions of bases exposed to interact with proteins)

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DNA helical structure is stabilized by

Hydrogen bonding between bases, hydrophobic and stacking interactions between base pairs, interactions of polyanionic backbone with cations

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Intercalating agents

molecules that fit exactly on rungs of DNA ladder - distort double-helix structure
Acridine dyes, Ethidium bromide, Doxorubicin

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Supercoiled DNA

adding (positive supercoiling) or subtracting (negative supercoiling) twists to double-helix - puts strain

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Topoisomerase inhibitors

inhibits ligase activity of type II topoisomerases - accumulation of DNA double strand breaks, causes cell death
Doxorubicin acts on human topoisomerase II - anticancer agent
Nalidixic acid and ciprofloxacin act on bacterial topoisomerase II - antibiotics