Mol Bio Midterm Review part 1

• 
• by Francis Crick

It was found that when heat-killed virulent bacteria was mixed in with avirulent bacteria, the mouse dies. This is due to the thick capsule gene being passed on from the virulent to the avirulent bacteria.

transformation

Transforming Principle = genetic material

• When pure DNA from a pathogenic (S) cell was isolated and added to a nonpathogenic (R) cell, this produced a pathogenic (S) cell after recombination and cell division.
• CapS = gene responsible for generation of a capsule, giving a smooth appearance

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Bacteria grown in 15N > 14N & harvested the cells after 1 & 2 generations. DNA was isolated and density gradient centrifugation was performed. After transfer to the regular media, there was only 1 band of DNA after 1 generation indicating a 15N-14N hybrid. There were 2 bands (15N-14N & 14N-14N) after 2 generations. These results indicate DNA replication is semiconservative.

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• RNA polymerases 
• (transcribe RNA from DNA)

DNA & nucleotides ATP, UTP, GTP, CTP

1 strand of DNA

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that RNA is synthesized in the nucleus & then localized in the cytoplasm.

the entire genetic complement of a living organism that contains the biological info needed to construct & maintain a living example of that organism

• made of DNA in most organisms
• made of RNA in some viruses

• nucleoside = base + sugar
• nucleotide = base + sugar + phosphate (1 or 2 or 3)

• phosphodiester;
• 3' of the sugar of one nucleotide to the 5' of the next nucleotide's sugar

There is a polarity in the structure of each strand, starting at 5' phosphate & ending with the 3'-OH on the other end.

In one strand of DNA, nucleotides can be arranged in any order (any nucleotide can follow the same or any other nucleotide)

the angles of glycosidic bonds.

One one side of each glycosidic bond the less open angle is ~120 degrees (minor) & on the other side of it, it is ~240 degrees (major)

• Major;
• they are wider so there is more room for interaction

of additional hydrogen bonds (donor & acceptor & hydrophobic bonds (Vander Waals) between DNA & other molecules (proteins)

• the average conformation of the double helix seen in physiological conditions
• right handed
• Depending on the sequence of DNA, may change to some extent affecting the major & minor grooves

• double helix conformation that sometimes occur in DNA protein interactions
• more similar to RNA if it makes a double strand structure
• right handed
• wider helical diameter than B-form so more # of bases per complete turn
• lower rise per base pair, so shorter distance per complete turn

• separation of the strands of DNA from each other
• can happen by breaking hydrogen bonds by high temp or high pH

• The 2 strands can be reattached if the temp or pH are brought down.
• This reattachment is by restoration of hydrogen bonds.
• For hybridization to occur, both strands should be complementary.

• less (40%);
• the stack of bases in double stranded DNA that makes them unavailable to UV;
• rapid increase in absorption

Thus it is possible to determine the melting point of DNA (Tm)

• size of DNA (number of bases) - short DNA fragments have lower melting points
• GC content - Higher GC = more hydrogen bonds = higher melting point. Also in base pair stacks, G:C has more interaction with adjacent base pairs.
• Ionic strengths - Higher salt concentration = higher melting point. High levels of positively charged ions surround the negatively charged phosphates in DNA backbone, therefore it is easier for both strands to not repel each other.

long & linear (DNA molecules + their associated proteins)

circular

(also genetic material of some viruses & DNA of mitochondria)

independent circular DNA mostly found in bacteria, but not considered to be part of their genome

twist number (Tw)

writhe number (Wr)

• Opening the 2 strands;
• Postive;
• Negative

linking number (LK)

If there is no writhe, the cccDNA (covalently closed circular DNA) is called relaxed. (Lk⁰ = Tw + 0)

• LK = Tw - Wr > LK < LK⁰;
• LK = Tw + Wr > LK > LK⁰

super helical density (σ) is calculated

σ = ΔLK/LK⁰

• phosphodiester;
• topoisomerase;
• decreases

introduces a break in one strand's phosphodiester bond (a nick) & passes the 2nd strand through the generated gap. The 2 ends of the broken strand are realigned.

breaks both strands of the double helix, creating a "gate" through which a 2nd segment of the double helix is passed.

Unlike topoisomerase I, this requires the use of ATP.

• gyrase;
• induces negative supercoil which is favorable for DNA replication & transcription

DNA topoisomers: circular DNA of the same size but different LK

Relaxed circular DNA moves slower in gel electrophoresis than linear DNA. Supercoiled DNA moves faster as it is more compact. The more supercoiled, the faster it moves.

• 2'OH;
• A-DNA (wide shallow minor grooves & narrow deep major grooves);
• minor

Since the minor groove doesn't have much chemical info, it is not well suited for sequence specific recognition of RNA.

relaying on the structure of hairpins, loops, bulges, & distortions of non-canonical base pairs (e.g. tRNA)