Nuclei Acid Structure and Chromosomes 1 Flashcards
how are nucleic acids formed?
5’-P is esterified by 3’-OH of another nucleotide to form a phosphodiester bond
what results from the nature of phosphodiester bonds?
- DNA and RNA have polarity/non-symmetrical bond
what direction is DNA written in?
5’ to 3’ direction
how are nucleic acids named?
- name bases using one letter code in 5’ to 3’ direction
what observations helped solve the structure of DNA? (4)
- Franklin: X-ray image suggested double helix structure
- Chargott rules: A = T =/= G = C
- Donohue: A-T (2-H bonds) and G-C (3-H bonds) can form H-bonds
- Furberg: bases are at right angles to sugars
what is the orientation and composition of the DNA helix? (2)
- DNA is a right handed double helix
- composed of polynucleotide chains
define how the DNA strands are complementary (2)
- A pairs with T; G pairs with C
- the sequence of one strand determines the sequence of the other
define how the DNA strands are anti-parallel
- the DNA strands run in opposite directions
- one is 5’ -> 3’ and the second is 3’ -> 5’
what are the two ways that describe how DNA strands are oriented with each other? (2)
- the 2 DNA strands are complementary
- the 2 stands are anti-parallel
what components of DNA are on the outside/inside?
- sugar phosphate backbone is on the outside
- the bases are on the inside of the helix
how are bases oriented to the DNA helix axis?
- bases are almost perpendicular to the helix axis
how much are DNA bases separated by?
- separated by 3.4 A
how long is the repeating DNA helix section and how many bases are in each turn of these repeating DNA helixes? (2)
- repeats itself every 34 A
- 10.5 bases per turn of helix
what is the diameter of the DNA helix?
- 20 A
what are the three known forms of DNA?
- B-DNA
- A-DNA
- Z-DNA
what is the form of carbon in the sugars of B-DNA?
- C-2’ form of sugar
how is B-DNA generally characterized? (3)
- hydrated DNA
- most abundant form of DNA
- geometry describes “relaxed state” of DNA
how is A-DNA generally characterized?
- dehydrated DNA that is essentially a squished version of B-DNA
how is Z-DNA generally characterized?
- unstable and transient, making it hard to isolate or study
what forces hold DNA together? (4)
- H-bonds between bases (A-T, C-G)
- stacking of bases
- hydrophobic interactions
- electrostatic repulsion of phosphates
how do proteins access DNA bases? (2)
- major groove
- minor groove
what groove do proteins interact with more often and why?
- major groove because more functional groups are exposed here
how do proteins interacts with DNA?
- via H-bonds between side chains of amino acids and bases
what are the characteristics of RNA? (2)
- usually single stranded, but some parts can be double stranded
- can have very complex structure
DNA denaturation
- separation of DNA strands
how can DNA be denatured? (2)
- increasing temperature (easiest)
- changing pH
what determines the melting temperature of DNA?
- the temperature where half of the DNA molecule is single stranded
DNA renaturation
- previously denatured strands will reanneal to form original DNA molecule if conditions are reverted back to normal
linking number (2)
- how many times strands are wrapped around each other
- changing the linking number in DNA will create supercoils
overwinding DNA (2)
- positive supercoils
- increase in the linking number
underwinding DNA (2)
- negative supercoils
- decreases linking number
topoisomerase
- enzymes that change topology/linking number of DNA
whats are some of topoisomerases’ functions (2)
- primary way of packing DNA for bacteria’s circular genomes
- implication in DNA replication and transcription where separation of strands creates supercoils that need to be resolved
type I topoisomerases (2)
- change linking number by +/- 1
- does not require ATP
how do type I topoisomerases function? (3)
- make a ss break in DNA using tyrosine as a catalyst
- pass second strand through ss break
- reseal ss break
type II topoisomerases (2)
- change linking number by +/- 2
- require 2 molecules of ATP
how do type II topoisomerases function? (3)
- making ds break
- pass dsDNA fragment through dsDNA break
- broken DNA is re-ligated and 2nd DNA segment is released
bacterial DNA gyrase
- type of type II topoisomerase that decreases linkage number by 2
how is DNA packaged in bacteria? (2)
- circular genome with supercoils created by topoisomerases
- histone-like proteins help DNA supercoiling
how is DNA packaged in eukaryotes? (2)
- DNA forms complex with proteins to form chromatin
- chromatin is further packaged into chromosomes
nucleosomes (2)
- basic unit of chromatin
- made up of DNA “wrapped” around histones
histones (2)
- composition
- function of composition
- contain high percentage of basic amino acids, lysine and arginine
- lys and arg allow electrostatic interactions to form between histones and negatively charge DNA
