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CMB Block > Self Study- Nucleotide/DNA Structure > Flashcards

Self Study- Nucleotide/DNA Structure Flashcards

1
Q

Genome vs

Chromosome vs

Genes vs

Non-coding DNA

A
  • all genetic info
  • independent domains of genetic info
  • coding DNA/DNA transcribed to direct RNA transcription (20-25k proteins)
  • Regulate gene expression + unknown function
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2
Q

DNA transformation

(and evidence DNA carries biological info)

A

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)

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3
Q

Classify nucleotides as purine/pyrimidine and # of rings

A

Adenine/guanosine are purine (2 ring)

cytosine/thymine/uracil are pyrimidine (1 ring)

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4
Q

What has base + pentose?

+ phosphate?

Also list names as examples

A
  • 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)
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5
Q

Explain base stacking in DNA double helix

A

hydrophobic bases stack to interact with each other via H bonds and avoid water

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6
Q

What are the base pairs and how many H bonds do they have?

A

A/T (2 H bonds)

G/C (3 H bonds)

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7
Q

What does phosphate interact with on DNA?

A

H+ in water (making DNA acidic)

Mg2+ at physiological salt conc., shielding phosphate groups from have electrostatic intrastrand repulsion and separating DNA chains

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8
Q

DNA ligase

A

forms phosphodiester bonds between free 5’ and 3’ ends of DNA

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9
Q

Enzymes made of? Catalyst? Active site? Substrate-binding site? Catalytic site?

A

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

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10
Q

Nucleases

Exonucleases

Endonucleases

Restriction endonucleases

A
  • hydrolyze phosphodiester bonds
  • cleave last nucleotide at either terminal
  • cleave interior of polynucleotide
  • cleave only with specific base sequences
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11
Q

A-DNA

B-DNA

Z-DNA

A
  • DNA-RNA hybrid during transcription
  • Watson/Crick primary conformation in cells
  • zigzag, in DNA sequences controlling gene transcription
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12
Q

Denaturation

Annealing

Open-stranded bubbles

which base pairs separate more often?

When does denaturation occur?

A
  • 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
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13
Q

DNA supercoil purpose

topoisomerases

Type I

Type 2

Gyrases

A
  • 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)
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14
Q

Nalidixic acid

novobiocin

topoisomerase-targeted drugs

A
  • 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
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15
Q

Where does DNA bending occur?

A

Sites where proteins bind Also due to photochemical damage, can be a recognition signal for DNA repair

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16
Q

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?

A
  • 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
17
Q

Histones/HU proteins

Histone octamer protein & interaction site

H1 function

A
  • 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
18
Q

Nucleosomes (DNA turns? components?)

Chromatosomes (DNA turns? components?)

Linker DNA

Nucleofilament

Chromosomes

A
  • 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)
19
Q

Chromatin? (Where in non-dividing vs dividing cells?)

Centromere?

Telomere?

A
  • 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
20
Q

HU Proteins?

Nucleoids?

A
  • Prokaryotic histone-like proteins
  • Compacted form of bacterial chromosomes by interaction w/ HU proteins, RNA, cations, polyamines, and other non-histone proteins
21
Q

Inverted repeat vs mirror repeat vs direct repeat

A
22
Q

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?

A

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

23
Q

Introns (which genes have none?)

Exons

Splicing

Are introns in prokaryotes or yeast?

A
  • 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

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