Module 2: Section 3 - Nucleotides and Nucleic Acids

All nucleotides contain C, H, O, N and P

DNA - deoxyribose, phosphate group and a nitrogenous base - adenine, thymine, cytosine and guanine, double stranded

RNA - ribose, phosphate group and a nitrogenous base - adenine, uracil, cytosine and guanine, single stranded

A and G are purines - two rings

C, T and U are pyramidines - one ring 

A purine always pairs with a pyramidine

• Made up of many nucleotides joined together with phosphodiester bonds - forms the sugar-phosphate backbone
• In between the two strands are the nitrogenous bases (A, T, C, G)
• The bases always pair up to form complementary base pairs - adenine always pairs with thymine with two hydrogen bonds, and cytosine always pairs with guanine with three hydrogen bonds
• The two DNA strands are antiparallel, which means that the third and fifth carbons on the deoxyribose sugar are facing in opposite directions
• As the two DNA strands twist, a double helix shape is formed

Synthesis

• The hydrogen (H) from the hydroxyl group on carbon 3 of the sugar of one nucleotide, and the hydroxyl group from the phosphate group of the other nucleotide are removed
• A nucleotide and a molecule of water are formed
• This is a condensation reaction
• A phosphodiester bond forms between carbon 3 of the sugar and the phosphate group
• When many nucleotides are joined in this way, the resulting polymer is called a polynucleotide

Breakdown

• To break the phosphodiester bond, a molecule of water is added to the bond, which adds a hydrogen atom to the carbon 3 of the sugar and a hydroxyl group to the phosphate group
• This is a hydrolysis reaction

1. Break up the cells using a blender

2. Make a solution of detergent, sodium chloride and distilled water

3. Add the cells to a beaker containing the solution and incubate in a water bath at 60 degrees celcius for 15 mins - detergent breaks cell membranes, salt clumps DNA together, temperature of water should stop the enzymes in the cell form working and breaking down the DNA

4. Place in an ice bath and filter when cool. Place in a clean boiling tube

5. Add protese enzymes (break down some of the proteins) and RNase enzymes (break down RNA)

5. Dribble cold ethanol down the size of the tube so it forms a layer in top of the DNA-detergent mixture

6. DNA will form a white precipitate

The structure of ATP

• ATP has a similar structure to an RNA nucleotide
• It has a nitrogenous base (adenine), a ribose sugar and three inorganic phosphate groups

Uses of ATP

• Active transport across plasma membranes - ATP provides the energy for the carrier proteins to change shape and transport molecules against their concentration gradient
• Muscles - ATP is attached to actin filaments in the muscle and provides energy for the muscle to contract
• Glycolysis in cells - ATP provides the energy for pyruvate to be formed from triose phosphate

ATP as an intermediate energy store 

• ATP is synthsised from ADP and Pi using the energy from an energy-releasing reaction (eg. breakdown of glucose in respiration)
• ADP is phosphorylated to form ATP and a phosphate bond is formed
• Energy stored in the bond - released when bond is broken 

DNA replication is semiconservative - new DNA always contains one strand of the original DNA, and one strand of new DNA

1. DNA unwinds (catalysed by gyrase) and unzips (catalysed by helicase)

2. Both strands are used as templates and hydrogen bonds form between free DNA nucleotides and exposed bases through complementary base pairing (A → T, C → G)

3. Catalysed by DNA polymerase

4. The leading strand is synthesized continuously (DNA polymerase works in the 3’ to 5’ direction of the original strand), whereas the lagging strand (5’ to 3’ direction) is synthesised in fragments (known as Okasaki fragments) which are later joined, catalysed by ligase enzymes

5.The phosphate-sugar backbone is formed by hydrolysis 

6. Two identical DNA molecules are formed that are identical to the original DNA molecule 

mRNA 

• Made in the nucleus
• Three adjacent bases called a codon
• Carries the genetic code form the DNA in the nucleus to the cytoplasm, where it's used to make a protein during translation

tRNA

• Found in the cytoplasm
• Has an amino acid binding site at one end and a sequence of three bases at the other - anticodon
• Carries the amino acids that are used to make proteins to the ribosomes at translation

rRNA

• Forms two subunits in a ribosome (along with proteins)
• The ribosome moves along the mRNA strand during protein synthesis
• The rNA helps to catalyse the formation of peptide bonds between the amino acids 

Near universal - in almost all living organisms the same triplet of DNA bases codes for the same amino acid

Degenerate - for all amino acids there is more than one base triplet - may reduce the effect of point mutations as a change in one base of the triplet could produce another base triplet that still codes for the same amino acid

Non-overlapping - read from a fixed point in groups of three bases

1. The hydrogen bonds between the complementary bases break and the DNA uncoils thus separating the two strands

2. One of the DNA strands is used as a template by RNA polymerase to make the mRNA molecule (coding strand)

3. Free nucleotides line up by complementary base pairing and adjacent nucleotides are joined by phosphodiester bonds made by RNA polymerase thus forming  single stranded molecule of mRNA

4. mRNA then moves out of the nucleus through a pore and attaches to a ribosome in the cytoplasm which is the site of translation

1. mRNA attaches to a ribosome and tRNA collects amino acids from the cytoplasm and carries them to the ribosome. tRNA is a single stranded molecule with a binding site at one end thus it can only carry one type of amino acid, and a triplet of bases at the other 

2. tRNA attaches itself to mRNA by complementary base pairing - two molecules attach to mRNA at a time

3. The amino acids attached to two tRNA molecules join by a peptide bond and then tRNA molecules detach themselves from the amino acids, leaving them behind

4. This process is repeated thus leading to the formation of a polypeptide chain until a stop codon is reached on mRNA and ends the process of protein synthesis