1. Note 17 – SBI4U September 27th 2018
Nucleic acids
Note 17 – SBI4U
September 27th 2018

2. What do you remember about dna from grade 11?
eicacids
Password: sbi4u

3. Nucleic acids Two types: DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)
Both are polymers  long chain molecules made up of repeating smaller molecules (monomers)
These monomers are called nucleotides
Nucleotide: Sugar + base + phosphate
DNA stores hereditary info, determines structure and function of cells and can produce identical copies of itself to reproduce
RNA reads DNA’s info and transports it to be coded by the ribosomes
Originally named this way because they were discovered in the nucleus of the cell in 1869, the acid part comes from the fact that the molecules had phosphate groups in them so they were associated with phosphoric acid or H2PO4
Other nucleic acids that are similar in structure to the original 2 nucleic acids DNA and RNA are ATP, NADH, FADH2 and NADPH which are important in glycolysis pathways
ATP (adenosine triphosphate) energy molecule, when we have extra energy, you store it in bonds in ATP
Adenine, ribose sugar, 3 phosphates – bond contains lots of energy, when we need it we break the bond btwn 2 phosphates and release energy so our cells can use it – think of it like energy currency or money for your cells (store it in the bank when you make money, when you need it, you spend it)

4. atp Adenosine (adenine base) triphosphate
Made of a ribose sugar and 3 phosphates
Not a polymer, but considered a nucleotide
The “energy currency” of the cell  energy stored or released through the building or breaking of phosphate bonds
ATP (adenosine triphosphate) energy molecule, when we have extra energy, you store it in bonds in ATP
Adenine, ribose sugar, 3 phosphates – bond contains lots of energy, when we need it we break the bond btwn 2 phosphates and release energy so our cells can use it – think of it like energy currency or money for your cells (store it in the bank when you make money, when you need it, you spend it)

5. Central dogma of molecular biology
DNA  RNA  Proteins
DNA is transcribed into RNA
RNA is translated into proteins

6. DNA Lacking an O2 atom at the 2nd Carbon Function:
The genetic information of a cell
Located exclusively in the nucleus
Works with RNA to regulate the
primary structure of amino acids in proteins
Structure:
A double-helix structure made up of:
An alternating sugar-phosphate backbone
Deoxyribose is a 5-carbon (pentose) sugar
The “rungs” of the ladder: 4 nitrogenous bases
Confined to the nucleus because it is a large molecule and can’t fit outside of the nuclear pores in the membrane around the nucleus in order to get out to the ribosomes where proteins are made
Lacking an O2 atom at the 2nd Carbon

7. Nitrogenous bases
DNA is made up of 4 nucleotides (aka nitrogenous bases)
Adenine (A)
Cytosine (C)
Thymine (T)
Guanine (G)
Complementary base pairing
A pairs with T
C pairs with G
DNA is a double helix, 2 identical sides that are repeated sugar and phosphate molecules, middle rungs are nitrogen base pairs
A always pairs with T and C always pairs with G – that is, they are complementary to one another

8. RNA
Smaller nucleic acid where the central sugar of each nucleotide is ribose
Has 4 nucleotides, like DNA
However, thymine (T) is replaced by uracil (U)
All the others are the same
Adenine (A) binds to uracil (U)
Cytosine (C) binds to guanine (G)
In the cytoplasm, RNA is “translated”
into an amino acid sequence by ribosomes
RNA is made and is small enough to get through and be decoded into the protein that the DNA coded for
RNA is a single-standed “copy” of the DNA molecule
It’s a different sugar – ribose, but still has a sugar phosphate backbone to it as well
Thymine is replaced with uracil

9. Sugar groups in DNA vs rna

10. DNA VS. RNA 5 5 1 1 4 4 2 3 3 2 1 always binds to base
3 and 5 are phosphate
2 is different

11. DNA Bonding
The 2 strands of DNA in the helix are held together by hydrogen bonds between nitrogenous bases on adjacent strands
Each strand of DNA has a free phosphate group at one end and a free sugar at the other
These bonds only work if the strands are antiparallel (running in opposite directions relative to one another)
Phosphate lines up with sugar
Purines face pyrimidines to accommodate this
Nitrogen in bases and 1st carbon of sugar are held together by a covalent glycosyl bond

12. Nucleotide structure Pyrines  Larger, 2 carbon-ringed compounds
Pyrimidines  1 carbon-ringed compounds
A and G have 2 rings of Carbon – purines (pUrine – doUble)
1 ring of carbon – pyramidines (pyrImIdIne – sIngle)
2 H bonds between A and T, 3 between C and G – easier to break apart
Explains structure of DNA (watson and crick, won nobel prize), that’s how they determine which base can bond to which

13. Hydrogen bonding in nucleotides
Adenine & thymine (2 H bonds)
Cytosine & guanine (3 H bonds)

14. DNA Bonding Phosphate acts as a bridge
5th carbon on sugar bonds to –OH group of next sugar
These strands are “antiparallel” to one another
The fifth (5′) carbon from the sugar of one nucleotide is connected to the hydroxyl group attached to the third (3′) carbon of the next sugar with the phosphate group serving as the bridge between the two nucleotides. All of the phosphate groups for a strand have the same orientation so each DNA strand is said to have directionality with a 5′ end and a 3′ end. The two strands are in opposing directions to each other or said to be antiparallel.

15. Nucleotide bonding
Nucleotides in a single strand (polymer) of nucleic acid join together through a phosphodiester bond
Covalent bond between the phosphate of one nucleotide and the –OH group of another at the 3rd carbon
Condensation reaction between 2 –OH groups
-OH hydroxy group
In RNA, they coil into a helix but are still single stranded
DNA is synthesized 5’ to 3’ by DNA Polymerase but read 3’ to 5’
Phosphate group is highly charged, extremely polar group, negatively charged oxygens that are very electronegative (want more electrons to complete their octet)
Add phosphate adds a 2- (add as review)
ADD GLYCOSYL BOND

16. Finish the following drawing based on the pattern we discussed.
Try it out!
Finish the following drawing based on the pattern we discussed.

17. Why does this structure matter?!
Allows DNA molecule to be extremely stable  a necessary factor for a molecule that carries the genetic blueprint of an organism!
Phosphate bridges that link the sugars together are strong, maintaining the sugar-phosphate backbone
Weaker hydrogen bonding between the base pairs keeps the two strands together
Hydrophilic and hydrophobic regions of the molecule keeps the sugar-phosphate backbone on the outside and the nitrogenous bases on the inside
Structure dictates function!!
DNA needs to unwind during protein synthesis/replication, so weaker bonds are necessary

18. Homework for the weekend
P. 216 #1-4 in your textbook
The following is a segment taken from a strand of DNA:
5’-ATGCCTTA-3′
Write out the complementary strand for this segment. Be sure to show directionality.
You are given a sample of double-stranded DNA which contains 20% thymine. Calculate the percentage of adenine, guanine and cytosine in the molecule.