Self Study- Nucleotide/DNA Structure Flashcards
Genome vs
Chromosome vs
Genes vs
Non-coding DNA
- all genetic info
- independent domains of genetic info
- coding DNA/DNA transcribed to direct RNA transcription (20-25k proteins)
- Regulate gene expression + unknown function
DNA transformation
(and evidence DNA carries biological info)
Changes due to intro of novel biological info via gene transfer
(discovered in experiment with S and R pneumonococcus, when DNA from S was taken up by R, R transformed to S)
Classify nucleotides as purine/pyrimidine and # of rings
Adenine/guanosine are purine (2 ring)
cytosine/thymine/uracil are pyrimidine (1 ring)
What has base + pentose?
+ phosphate?
Also list names as examples
- nucleoside (ribose for RNA, deoxyribose for DNA, i.e. adenosine or deoxyadenosine)
- nucleic acid (i.e. adenylic acid, can have 1-3 phosphates, AMP to ATP)
Explain base stacking in DNA double helix
hydrophobic bases stack to interact with each other via H bonds and avoid water
What are the base pairs and how many H bonds do they have?
A/T (2 H bonds)
G/C (3 H bonds)
What does phosphate interact with on DNA?
H+ in water (making DNA acidic)
Mg2+ at physiological salt conc., shielding phosphate groups from have electrostatic intrastrand repulsion and separating DNA chains
DNA ligase
forms phosphodiester bonds between free 5’ and 3’ ends of DNA
Enzymes made of? Catalyst? Active site? Substrate-binding site? Catalytic site?
protein (and some catalytic RNA) has substrate binding site and catalytic site to determine specificity, where substrate binds has catalytic residues that act on substrate
Nucleases
Exonucleases
Endonucleases
Restriction endonucleases
- hydrolyze phosphodiester bonds
- cleave last nucleotide at either terminal
- cleave interior of polynucleotide
- cleave only with specific base sequences
A-DNA
B-DNA
Z-DNA
- DNA-RNA hybrid during transcription
- Watson/Crick primary conformation in cells
- zigzag, in DNA sequences controlling gene transcription
Denaturation
Annealing
Open-stranded bubbles
which base pairs separate more often?
When does denaturation occur?
- 2 chains separate (occurs in replication and translation)
- bases pair again
- sections where strands separate
- A/T (less H bonds)
- High temp, extreme pH/ionic strength
DNA supercoil purpose
topoisomerases
Type I
Type 2
Gyrases
- allow DNA to package in cell and take up less size
- enzymes that regulate superhelices (break and rejoin DNA strands)
- break 1 DNA strand and rotate to relieve supercoil
- break both strands, requires ATP
- relieve supercoiling from unwinding DNA (separating DNA strands of 2 chromosomes after replication/transcription)
Nalidixic acid
novobiocin
topoisomerase-targeted drugs
- antibiotic in UTI, interferes in breakage/rejoining of DNA by gyrases
- blocks binding of ATP in type II topoisomerases
- convert topoisomerases into DNA-breaking agents by interfering with ligase activity
Where does DNA bending occur?
Sites where proteins bind Also due to photochemical damage, can be a recognition signal for DNA repair
Cruciforms (Where? what do they control?)
Triplex DNA (Which bases? Where? Functions?)
Hoogsteen base pairing (Where? Role in Hereditary persistence of fetal Hb?)
Quadruplex DNA- Where?
- regions where interchain H bonds disrupted and intrachain H bonds form, control replication/transcription
- string of purine bases, functions in transcription control, start/stop of replication, telomere stability, binds in B-DNA major groove
- third strand forms H-bonds with another surface of double helix (not where Watson-Crick is), mutation blocking triplex DNA formation allows fetal Hb expression to continue un-repressed
- immunoglobulin genes that undergo recombination (diversity) + telomeres
Histones/HU proteins
Histone octamer protein & interaction site
H1 function
- basic protein complex associated with DNA (HU for prokaryotes)
- 2 of H2A/B, H3, H4, interact in minor groove
- stabilizes DNA which wraps around histone core
Nucleosomes (DNA turns? components?)
Chromatosomes (DNA turns? components?)
Linker DNA
Nucleofilament
Chromosomes
- 1 3/4 DNA turns, histone disk
- 2 DNA turns, histone disk + H1
- DNA between nucleosomes
- Linear arrays of nucleosomes and chromatosomes
- Series of looped, condensed domains of DNA fibers (condensed nucleofilaments)
Chromatin? (Where in non-dividing vs dividing cells?)
Centromere?
Telomere?
- DNA w/ associated proteins (nucleoproteins, both histone and non-histone). In nondividing, is dispersed within nucleus as lightly packed euchromatin and heavily packed heterochromatin). In dividing cells, condenses into chromosomes
- Site of attachment of the chromosome to the mitotic spindle
- Ends of chromosomes
HU Proteins?
Nucleoids?
- Prokaryotic histone-like proteins
- Compacted form of bacterial chromosomes by interaction w/ HU proteins, RNA, cations, polyamines, and other non-histone proteins
Inverted repeat vs mirror repeat vs direct repeat
Structural Genes?
How many bp in human genome?
How much of human genome is coding sequences?
What is remaining DNA function?
How far apart are eukaryotic genes on average?
DNA coding sequences for proteins
3.5x109 bp
Less than 10% of human genome
Control gene transcription, make up centromeres/telomeres, mostly unknown (may function during development)
40 kb apart
Introns (which genes have none?)
Exons
Splicing
Are introns in prokaryotes or yeast?
- Nucleotide sequences that interrupt coding sequences (histone genes have none)
- Coding sequences found in final mature mRNA
- Removing the introns from original gene transcript
- No, rarely
