Lecture 1 (in progress)

*List the important properties of DNA (5)

1. Stores information compactly

2. Must be copied precisely

3. Information must be accessible to be copied into RNA

4. Must be stable (DNA in daughter cells must be identical to DNA in parental cells)

5. Must go through change mutagenesis at a low rate

*What are the 3 parts of a DNA nucleotide? + draw the DNA nucleotide + draw the different carbons and what parts they’re attached to + which bonds?

1. Deoxyribose sugar - A 5-carbon sugar (5 sides)

• 1’ carbon:

  • Oxygen connects the 1’ carbon to the 4’ carbon

  • nucleotide base is attached to the 1’ carbon VIA covalent bond

• 2’ carbon:

  • Hydrogen at 2’ carbon (which is why it’s called a DEOXyribose, without oxygen)

• 3’ carbon:

  • OH (hydroxyl) group attached to 3’ carbon

    • OH has phosphodiester bond with the next nucleotide

• 5’ carbon:

  • projects outward from the 4’ carbon

  • a phosphate is attached to the 5’ carbon

2. One nitrogenous base (A C T G)

3. Up to 3 phosphate groups

monophosphate

DNA nucleotide form when it is in a nucleotide chain

Triphosphate

DNA nucleotide that is free and not in a nucleotide chain

2 structures of nitrogenous bases

Pyriminidnes - single-ringed, C T

Purines - double-ringed, A G

dNMPs

Monophosphate forms of deoxynucleotides (DNA nucleotides)

N→ any of the four nucleotide bases (for example, Adenine base would be called dAMP, Guanine dGMP, etc…)

*WHEN DNA HAS 1 PHOSPHATE

dNTPs

Triphosphate forms of deoxynucleotides (DNA nucleotides)

N→ any of the four nucleotide bases (for example, Adenine base would be called dAMP, Guanine dGMP, etc…)

*WHEN DNA HAS 3 PHOSPHATES

NTP

When RNA has 3 phosphates

Draw a purine vs a pyrimidine nucleotide

MAIN IDEA: purine has 2 rings, pyrimidine has 1 ring

What bonds hold nitrogenous bases together?

Hydrogen bonds (they act like velcro)

How many hydrogen bonds hold A and T together?

2 hydrogen bonds

How many hydrogen bonds hold G and C together?

3 hydrogen bonds

What is the direction for template vs. new DNA strands?

Template strand runs from 3’ → 5’

New strand is synthesized from 5’ → 3’

this is so that the hydrogen bonds are stable between nitrogenous bases

DNA polymerase

enzyme that adds new nucleotides to the growing DNA strand

Explain the steps for DNA strand elongation

1. DNA polymerase forms a phosphodiester bond with the 3’ OH of one nucleotide and the 5’ triphosphate group of the incoming nucleotide

2. When this bond is formed, 2 out of 3 of the phosphates are removed from the incoming nucleotide

3. This extends the DNA strand

Why is DNA antiparallel?

So the hydrogen bonds between nucleotide bases are STABLE

Semiconservative DNA replication

if you replicate a DNA strand, one side of the replicated strand would be new, while the other side of the replicated strand would be old

conservative DNA replication

if you replicate a DNA strand, both sides of the replicated DNA would be new

dispersive DNA replication 

if you replicate a DNA strand, new and old DNA will be dispersed together on both sides

PCR

DNA replication that takes place in a test tube

PCR steps

1. Denaturation (mixture is heated to 95 degrees celsius → DNA denatures from double-stranded to single stranded) → (breaks hydrogen bonds)

2. Primer annealing (temperature is lowered to 45-68 deg celsius → lets primers attach to the DNA strands)

3. Primer extension (temperature is raised to 72 degrees celsius,