DNA Structure and Function Flashcards
Is DNA positively or negatively charged? How does this affect stability?
Negative
Enhances stability
How many H bonds between C and G?
3
How many H bonds between A and T?
2
Which carbon on a ribose contains the hydroxyl group?
C2
What are the purines?
Adenine
Guanine
Describe the appearance of guanine
Bulky, carbonyl
Describe the appearance of adenine
Bulky, amine
Describe the appearance of cytosine
Not bulky, amine
Describe the appearance of thymine
Not bulky, carbonyl
You always read a DNA sequence __’ to __’
5’ to 3’
How does the A form helix appear?
Bases appear twisted and larger/stretched
What are the stabilizing factors of DNA?
H bonds between bases
Van der Waals forces
Positively charged ions
Does single or double stranded DNA absorb light better?
Single stranded due to openness/exposure of bases
What is the melting temperature of DNA?
When 50% of the DNA is separated
Does AT-rich or GC-rich DNA require higher melting temps?
GC-rich
What are nucleoside reverse transcriptase inhibitors (NRTIs)?
Block HIV RNA from being reverse transcribed
lacks a 3’ hydroxyl
What is AZT?
an NRTI to fight HIV
What is acyclovir?
An anti-HIV drug that is converted by (virus-encoded) thymidine kinase into a nucleoside (gGTP) analog similar to AZT
(lacks a 3’ OH)
What is ciprofloxacin?
A quinolone (fluoroquinolone)
Used to treat a wide variety of infections agents (gram-negative AND gram-positive)
How does ciprofloxacin work?
Binds to DNA gyrase topoisomerase II (or IB) via a water metal ion (Mg2+) bridge
Inhibits the topoisomerase ligase activity leading to DNA fragmentation
Does DNA have to be cut and re-ligated to be supercoiled?
Yes
Type I topoisomerases can only work on DNA that is ______.
Strained
Do type II topoisomerases require ATP?
Yes
Does type I topoisomerase require ATP?
No, uses the energy of the strained DNA
What type of organisms use type II topoisomerases?
Bacteria, which is why Cipro only attacks bacterial not human DNA!
What are Type I topoisomerases used for?
Ovarian, colorectal, cancer (since type I will attack human DNA, this is the only useful purpose)
Which four histones make up the nucleosome core?
H2A, H2B, H3, H4
What is the function of H1 histone?
Holds the tertiary structure of the nucleosome together by binding to the linker DNA
Histones are ______ charged.
Positively
What is a solenoid?
6 nucleosomes per turn coiled with DNA to form a long fiber
mRNA is created based off the ______ strand and is thus the ___’ to ___’ strand.
Template 3’ to 5’
What type of mRNA/DNA is colinear? Why?
Prokaryotic mRNA/DNA because there are no introns/exons and thus the sequences are nearly identical
What are 3 traits of prokaryotic genes?
- DNA and protein are colinear
- Gene sequences are unique/not repeated
- Size of genome corresponds to number of genes
What are 3 traits of eukaryotic genes?
- Size of genome does not correspond to number of genes
- Most eukaryotic DNA is non functional or not unique
- About 10% of genome codes for proteins
How many repeats must genes have be to be considered a “highly repetitive sequence”?
> 300,000 copies/genome
What are some attributes of highly repetitive sequence?
Not transcribed
Usually short tandem AT rich repeats
Make up 10% or less of the genome
What is a prime example of a highly repetitive sequence?
Telomeres!
What are some attributes of moderately repetitive sequences?
Derived from transposons
Usually transcribed usually not translated
Make up 25%-45% genome
Code for highly used genes such as histones, rRNA, tRNA but mostly nonfunctional
Separates highly transcribed single copy DNA (i.e. LINES and SINES)
How many repeats are “moderately repeated sequences”?
2-300,000
What are unique or single copy sequences?
Make up 40-60% of genome - coding and noncoding
Only 1% of the genome is made into protein in any one cell
Some unique sequences can be related/grouped after a duplication and divergence (e.g. globulins, tubulins, actins) These are often tissue or developmentally regulated and can be clustered or dispersed
What are housekeeping genes?
Universally required genes
What are pseudogenes?
Non-functional unique sequences that arise by gene duplication
What is myotonic dystrophy type 1?
An autosomal dominant trinucleotide (CTG) repeat in which increased repeat-element copy number results in increased severity.
Age at onset decreases and the severity increases in successive generations (anticipation)
Trinucleotide repeats _____ than 49 are ______.
less than 49 = asymptomatic
What mistake leads to trinucleotide repeats?
Slippage during replication
What are some triplet repeat diseases?
Fragile X
Friedrichs Ataxia
Huntingtons
Myotonic dystrophy
