Exam 2 Molecular Biology Dr. Borgon

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