Unit 1 DNA structure

The ____ structure of DNA determine’s its ____

• antiparallel complementary structure

• function

Nucleotides are made up of

• sugar

• phosphate

• nitrogenous base

Nucleotides can contain 1,2 or 3 Phosphates what are they in DNA versus RNA

• DNA(deoxyribose)(lack a ‘OH)→ dNMPs, dNDPs, dNTPs

  • deoxy for d m for mono, di, trip

• RNA(ribose) → NMPs, NDPs, NTPs

Purines versus pyrimidines

• Purines are A and G

  • have 2 rings

• Pyrimidines are T,C, U

  • 1 ring like a pie

DNA primary structure

• deoxyribonucleotides

• Phosphodiester bonds (bw 3’ Oh and 5’ of next moleule) form the backbone of DNA

  • bw the 3’OH of the existing strand and the a-phosphate group of a dNTP

• 3’OH important bc it’s like the "anchor point" for adding new building blocks,

Draw the phosphodiester bond reaction

• Show nucleotide’s 3’OH being attacked by a nucloeitde that has 3 P’s on it instead of 1

• this forms a deoxyribonuclotide like the primary structure + PPi and H20

DNA secondary structure

• double helix→ 2 strands

• Has H bonds bw bases

• Complementary pairing

• Antiparallel strands → mechanism of replication (5’-3’ and 3’-5’)

What are the numeric facts about DNA secondary structure

• each nucleotide pair ~ o.34 nm

• 10 nucleotide pairs per turn

• 2 nm in diamter

• grooves bound by DNA binding proteins mostly bind the major groove

How is DNA structure different from RNA?

• DNA has 2’ H RNA has 2’OH

• RNA has U DNA has T → pyrimidine flavors different

• Secondary structures are different

  • RNA has flexible stem loop strucs (less stable) versus DNA stiff double helix (very stable)

  • RNA has different base pairing

How does DNA’s secondary structure support its function

Function= it’s hereditary material, it stores and transmits genetic information

1. Info is on the inside

2. H bonds are a goldilocks bond

• Weak enough to easily break apart and access info but strong enough to hold helix together and keep info stable/safe over long time

3. Information has redundancy

• Damage to 1 strand can be repaired by looking at the other strand (double stranded nature)

4. Double code offers additional space for info storage (either strand could be coding)

What does PCR do

• make copies of a specific segment of DNA

• amplifies DNA

• Why do PCR primers need to be complementary to the template DNA?

  Answer:

  • Primers bind to the template strand so DNA polymerase can extend from the 3' end, allowing amplification of the target sequence.

Basically 1. heat seperates the double strand DNA into single strands 2. primers (short DNA seqs) bind to the specific segment to be copied 3. taq polymerase (dna poly) copies the DNA creating new but identical strands 4. the process repeats doubling DNA in each cycle

The coding (sense) or non template strand ..

• has the same sequence as the primary RNA transcript

• replace t’s with Us

• goes from 5’-3’

• to make mRNA take the strand and just switch T→U 5’--blah3’

Template (antisense) strand

• has the complementary sequence to the primary RNA transcript

• 3’-5’ (bottom strand typically)

• So if given the template strand and I need the mRNA the template strand will go from 3’-5’ so make the complemntary code and write it from 5’-3’ with Us

  • makes sense bc the complementary sequence would give you the top (coding) strand which has the same sequence as the mRNA but with Us

Nucleic acid synthesis proceeds in the ___ direction and requires a __. It is used in

• 5’-3’ direction

• 3’OH

• Replicationm transcription, PCR, sanger sequencing

Show that double stranded nucleic acid structures are ANTIPARALLEL by drawing it

on onenote too