1 nucleic acids & nucleotides - purines, pyrimidines, nucleosides, nucleotides

what are the different functions of nucleotides and their polymers

• storage and decoding genetic information - DNA and RNA

• as enzymes - RNA

in later parts:

• oxidation-reduction reactions - Electron carriers within the cell as NADH/NADPH/FMNH2/FADH2

• energy transfer - Contain “high energy” phosphoanhydride bonds like ATP/NTP

• biosynthetic reactions - Coenzyme A

what are the 3 pyrimidine bases and how to identify them

• have 2 nitrogens at C1 and 3

• long name = small structure

• carbonyls at C2

• Uracil - in RNA, has another carbonyl at C4

• Thymine - In DNA, has another carbonyl at C4, has methyl group

• Cytosine - only pyrimidine that has 3 nitrogens

what are 2 purines and how to identify them

• short name = long structure

• 2 rings - one 5 carbon and one 6 carbon

• 4 nitrogens (2 in each ring) - N3 & 9 are separated by 1 carbon and N1 and 7 are seperated by 2 carbons

• adenine - doesnt have oxygen, 5 nitrogens

• guanine - carbonyl at C6

what is common between pyrimidines and purines

• There are other nitrogen bases, these are the ones commonly incorporated into DNA and RNA

• All the bases are aromatic and heterocyclic

what does resonance describe

describes delocalized electrons in molecules where the bonding cannot be expressed by a single Lewis structure

• Occurs in systems with neighboring pi-electrons (double bonds) or certain lone pairs

what do lone pairs in resonance cant do

• Lone pairs in resonance cannot accept hydrogen bonds because they are not localized

  • resonance stabilizes molecules but reduces hydrogen bonding capacity

  • you will always be told which structures have resonance and are aromatic

how many hydrogen bonds can pyrimidine bases make as acceptors and donors

uracil - accepts 4 times and donates twice

thymine - accepts 4 times and donates twice

cytosine - accepts 3 times and donates 3 times

*each oxygen has 2 lone pairs to accept

how many hydrogen bonds can purine bases make as acceptors and donors

adenine - accepts 3 times and donates 3 times

guanine - accepts 4 times and donates 4 times

*check slides 12, 13

what are two things incorporated into the different nucleic acids

• Ribonucleic Acid (RNA) - has OH in carbon 2 prime, C5 prime is the only carbon not apart of the ring structure

  • Polymer of G, A, C, U

  • Sugar portion is ribose

• Deoxyribonucleic Acid (DNA) - missing an oxygen

  • Polymer of G, A, C, T

  • Sugar portion is deoxyribose

what are nucleosides

• purine and prymidine bases linked to a 5 carbon sugar (pentose) to form a nucleoside, building block of nucleic acids

• carbons in sugar ring are numbered 1’ to 5’ to differentiate, always clockwise

• RNA has ribose sugar and DNA has 2’ deoxyribose

how do you name purine and pyrimidine nucleosides

-ine in purines become osine:

• adenine + ribose=adenosine

• adenine + deoxyribose= deoxyadenosine

• guanine + ribose= guanosine

pyrimidines now end in idine

• cytosine + ribose = cytidine ** cytosine ends in ‘osine’ but its a purimidine base not a purine nucleoside

• thymine + deoxyribose = deoxythymidine

• uracil + ribose = uridine

how do you make a phosphoester bond

• linkage between phosphate and hydroxyl group

• remove H from hydroxyl and OH from phosphate to remove water in dehydration and condensation reaction to give bond

what is a nucleotide

• a nucleoside linked to one or more phosphates

• ex. ATP

• named by taking nucleoside and adding the number of phosphates attached

• phosphates are usually added to C5’ OH if not it has to let reader know, is put in the name

what N’s are the sugar attached to in a purine and pyrimidine

Sugar attached to N1 in pyrimidines and N9 in purines

**see slides 21, 22, 25

what are the different names for (deoxy)nucleoside and (deoxy)nucleotides

is this a pyrimidine base

no its a nitrogen base but not pyrimidine