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Fridrich Miescher was studying
proteins
Phoebus Levene discovered
The base-sugar-phosphate
Frederick Griffith discovered
Transformation
Oswald Avery showed that
DNA was the genetic material via transformation
Erwin Chargaff discovered
A=T and G=C
Alfred and Martha Chase discovered that
Bacteriophage 32Penters the host and 35Sdoes not
At the time nucleotides were those to be
Bland and boring, whereas proteins were unique and exciting
Who did the experiment of the mice with the living R and S cells?
Frederick Griffith
The Avery, MacLeod, and McCarty Experiment determined that the only way to eradicate transformation was to..
Digest the material with an enzyme that, of all things, degraded DNA
Who was so impressed by Avery's results that he said he should win two Nobel Prizes?
Erwin Chargaff
William AstBury developed the idea of
A-helix and b-sheet worked on keratin
What did William Astbury accidentally do?
He took incomplete X-ray diffraction pictures of DNA and ended up interpreting DNA structure. He described DNA as "piles of pennies."
What did William Astbury discover that was correct?
He found out that the spacing between bases was 0.34 nm was equal to that of amino acids
What did William Astbury do before zRosalind Franklin?
He took a Photo 51 image before her
Linus Pauling discovered...
A-helix structure by ignoring the side chains and drawing the amino acid backbone on paper and folding it based on the data. This led him to propose a three chain model of DNA
James Watson worked on
Bacteriophage at Indiana University
Francis Crick designed
Naval mines for the British Navy
What did James Watsona nd Francis Crick believe?
They believed that DNA was the genetic material
Rosalind Franklin studied
Chemical structures and captured images of both A and B Form DNA.
By taking pictures of both A and B Form DNA what did she determine?
She was convinced that A DNA was not helical
What did we learn from Franklin's Photo 51?
We learned that DNA is an antiparallel structure
What is the analysis of Photo 51?
DNA would be helical or zigzags
Spacing shows 3.4 nm
Four diamond-shaped areas
Fourth missing post due to where chains crossed
What is the only thing that has changed about the structure of DNA since 1953?
The distance between pairs for DNA has been accurately measures to 0.332 nm
Purine consists of
Adenine and guanine
Pyrimidine consists of
Cytosine and thymine
Purine has how many carbon-nitrogen rings?
Two
Pyrimidine has how many carbon-nitrogen rings?
one
Nucleotides are made form
Various precursors
Purines are synthesized on
The ribose
Pyrimidines are attached
After the ribose
Ribonucleotides are converted into deoxyribonucleotides by a
Reductase
Nucleotide are found in
DNA
Nucleotide =
Nucleoside monophosphate
dNTP =
Deoxynucleotide triphosphate
Synthesis only occurs in the _'_' direction, template read in the _'_' direction
5'3' direction; 3'5' direction
Adenine to thymine has how many H-bonds?
two
Guanine to cytosine has how many H-bonds?
three
Tautomers of imino/enol are
Rare but can occur
DNA bases are in the
amino/keto conformation
Tautomers are a source of
Spontaneous mutations
DNA structure descriptions
Double helix
sugar/phosphate backbone
Deoxyribose
Base pairing
Antiparallel
major/minor groove
2 nm wide
34 Angstroms and 10.5 bp/turn
What did the MICA experiment consist of?
Involved binding DNA to MICA and digesting with an enzyme to determine the periodicity of DNA helix
What is the length of a minor groove?
12A
What is the length of a major groove?
22A
What is the reason for major/minor grooves?
DNA is not like a twisted ladder with equal sides
Sugars protrude at 120 or 240 degrees from the phosphate backbone
What does a major groove have more of than minor grooves?
More hydrogen donors and acceptors
Which groove can not be distinguished?
Minor groove
What do zinc fingers wrap around?
Major grooves
Proteins that bind to DNA probably have how many zinc fingers?
4-5 zinc fingers
Base-specific contact residues have
Variation and change a ton
Strong bonds are
B-S-P, 3'5' phosphodiester linkage
Weak bonds have
Two strands held together between complementary pairs (purine and pyrimidine)
What is dsDNA?
Flat surfaces of bases stack creating shared electrons between bases and limiting contact with water
What is ssDNA?
Unfavorable because pyrimidines are shorter than purines
Weak bonds play a critical role in
Determining the secondary and tertiary structures and functions of DNA, RNA, and proteins
Which base pair has good stacking?
G-C or C-G
Which base pair has bad stacking?
A-T or T-A
DNA is stabilized by
H-bonds and base stacking
Weak bonds can break but
Reform quickly
AT is ____ stable than GC and ____ likely to break
Less, more
AT is less stable than GC and more likely to break due to...
Lower base stacking, two H-bonds, and the ordering of water
Disulfide bridges are
Weak covalent bonds (still considered strong bonds though)
What does Tm stand for?
Melting temperature
Tm increases with ______, _____, and _______ _______
%GC, length, and salt concentration
At Tm____% bonds are broken and ____% are bound
50%,50%
What does GC content stand for?
Guanine-cytosine content
Larger genomes tend to have ______ GC
lower
Malaria is ____% AT
80%
The human genome has ____% GC
41%
DNA in the body is typically
Right-handed
A Form DNA information:
11 bp/turn, shorter. Found in lower humidity, may be used by phage by causing an A to B form expansion/contraction to drive packaging
B form DNA information:
10 bp/turn, longer. Can vary depending on the sequence, bur is a good approximation of DNA found in the cell
Z form DNA information:
12 bp/turn, longest, left-handed, often repetitive (G-C, C-G)
A and B form DNA are both ____-handed
Right
Z form DNA is _____-handed
Left
What percent of tumors need Z DNA to survive?
40%
Quadruple Helix is...
Guanine-rich, parallel and antiparallel conformations
Found at telomeres, replicated more quickly, and may turn genes on/off
Linked to unstable DNA/cancer
I-motif DNA is..
Cytosine-rich, found at promoters and telomeres, regulatory
T/F: DNA is flexible
true
__ in ______ is flipped out at any given moment
1 in 100,000
DNA can supercoil to form more
Complex topology
DNA can form supercoils when
Two dsDNA strands cross over one another
What can the supercoil be?
They can be plectonemic or toroidal (solenoid), negative or positive
Define linking number
The number of times one strand has to pass over the other to separate completely
Define twist
Number of turns of one strand over the other
Define writhe
Supercoiling
Equation for linking number
Twist + writhe = linking number
DNA with negative supercoiling is _____-handed
Right
DNA with positive supercoiling is ____-handed
left
Negative supercoiling has
Unwinding, underwinding, subtractive twisting
Positive sueprocil is found in
Thermophiles
Positive supercoil has
Tighter winding, overwinding, restricted access
Negative supercoiling on a nucleosome is _____-handed
left
Positive supercoiling on a nucleosome is ____-handed
right
DNA is usually _____, and this is controlled by enzymes
compact
What happens in topoisomerase?
ss/ds breaks, changes supercoiling
Gyrase bacteria introduces ______ supercoils and relaxes _______ supercoils
Negative; positive
Function of helicase
Separates two strands of DNA during synthesis, transcription, recombination,r repair
Function of topoisomerase
Relax DNA twist and write, detangle DNA during replication and recombination, relieves tension during rpelication
What is Type I topoisomerase?
ssDNA cuts, steps of +/-1, works at replication fork and transcription, removes +/- supercoils, produces right-handed solenoid supercoils in humans
