Exam 4: Nucleic Acids Flashcards
Noncoding DNA sequences
DNA that does not code for proteins (Spacer sequences, Introns, Genes encoding nonprotein-coding RNAs, Repetitious DNA)
Spacer sequences
DNA sequences that separate genes
Introns
Noncoding sequences within gene - spliced out of primary RNA and transcribed into mRNA or protein
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
Exons
sequences of DNA translated into protein
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
pseudogene
Gene family duplicate that was inactivated by mutation
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
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
Chromosomes
DNA organized into large linear molecules
in division each chromosome consists of two identical DNA strands - chromatids - attached to each other at centromeres
Chromatid
identical DNA strands attached to form chromosome during G2 & M phases of cell cycle
Telomeres
special sequences at ends of chromatids
DNA forms a loop to protect free end from degradation
Haploid
cells containing one copy of each chromosome
In humans only egg and sperm are haploid
Diploid
cells containing a maternal and paternal copy of each chromosome - homologous chromosomes
Mitochondrial genome
different from nuclear genome
Circular, multiple copies per organelle
not extensively associated with proteins
Nuclear envelope regulates
Access of proteins to DNA;
Separation of translation and transcription - allows for post-transcriptional modification of RNA
Heterochromatin
intensively stained on electron micrograph - complexed with proteins, highly condensed, and transcriptionally inactive
Located on periphery of nucleus
Euchromatin
translucent on electron micrograph - transcriptionally active, decondensed DNA, not associated with as much protein
Nucleolus
large, intensely stained area on electron micrograph - internal structure, contains genes encoding ribosomal RNA
Actively transcribed
nuclear matrix
protein scaffold that attaches to chromosomes
Chromosomal territory
each chromosome occupies a distinct territory of nucleus
Interchromosomal domains
separate chromosomal territories
Nuclear envelope
double-membrane, contiguous with endoplasmic reticulum
contains nuclear pores - only way to enter nucleus
Nuclear pore
regulate traffic between nucleus ad cytoplasm
Energy-dependent to transfer proteins into nucleus
3 main types of large molecues that must be actively and selectively transported into/out of nucleus
mRNA, proteins, ribosomal subunits
Ran
small GTP binding protein that mediates import and export from nucleus
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
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
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
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
Primase
primer to initiate DNA replication, made of RNA
degraded by exonuclease - not in final DNA product
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
DNA helicases
unwind DNA double helix using free energy of ATP hydrolysis
Start at origins of replication
Single-stranded binding proteins
bind to exposed single strands of DNA to prevent from re-associating
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
DNA polymerase alpha
synthesizes short RNA primer - primase activity
Sliding clamp accessory proteins
adjacent to primer on DNA - allow enzyme to synthesize more DNA before falling off template
DNA polymerase epsilon
synthesizes DNA on leading strand (toward growing replication fork) - synthesized continuously in 5’ to 3’ direction
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
DNA ligase
joins together Okazaki fragments - requires ATP
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
Purine
Adenine and Guanine
Pyrimidine
Thymine (Uracil in RNA) and Cytosine
Guanine-cytosine forms
3 hydrogen bonds
Adenine-thymine forms
2 hydrogen bonds
Most protein-DNA interactions take place via
major groove (portions of bases exposed to interact with proteins)
DNA helical structure is stabilized by
Hydrogen bonding between bases, hydrophobic and stacking interactions between base pairs, interactions of polyanionic backbone with cations
Intercalating agents
molecules that fit exactly on rungs of DNA ladder - distort double-helix structure
Acridine dyes, Ethidium bromide, Doxorubicin
Supercoiled DNA
adding (positive supercoiling) or subtracting (negative supercoiling) twists to double-helix - puts strain
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
