Nucleotides 2.1.3

What is a nucleotide

A monomer of DNA or RNA

What is a Purine

2 carbon ring structure (Adenine and Guanine)

1 carbon ring structure (Cytosine, Uracil and Thymine)

How many H bonds between A and T

2

How many H bonds between C and G

3

Condensation reactions in nucleotides

Forms phosphodiester bonds to create a polymer

What is the polymer of nucleotides called

Called a polynucleotide. A phosphodiester bond is a strong covalent bond that forms between the pentose sugar and phosphate of another nucleotide

ATP Structure

Contains three phosphate ions that play a significant role in energy transfer

Essential for metabolisms

Is an immediate source of energy for biological process

How is ATP made

Made during respiration via a condensation reaction and using the enzyme ATP Synthase

ADP + Pi —> ATP + H2O

ATP is also hydrolysed using Enzyme ATP hydrolase

ATP + H2O —> ADP + Pi

Breaking the bond of one of the phosphate groups releases small amounts of energy

What is phosphorylation

When the inorganic Phosphate made from hydrolysis of ATP binds to a different compound to make them more reactive

What can DNA code for

The sequence of amino acids in the primary structure, This determine the final 3D structure and function of the protein

Polymer forms a double helix with H bonds in between

How DNA structure relate to its function

Stable structure due to sugar phosphate backbones and double helix

2 strands so replication can use both strands

Weak H bonds broken down by helicase enzyme

Large molecule that carries a lot of information

Complementary base pairs means identical copies can be made

DNA Precipitation

1- Homogenise cell with detergent, breaks open cells and cell membranes therefore releasing its contents

2- Filter and remove large debris

3- Add salt to break H bonds between DNA and water

4- Add protease to digest the proteins

5- Add ice cold ethanol to create a precipitate of the DNA (White strand)

Types of RNA

mRNA details

A copy of one gene from DNA

Created in the nucleus carry a copy of the genetic code to the ribosomes in the cytoplasm

mRNA shorter than DNA, short lived, single stranded and every 3 bases in sequence code for one specific amino acid, these 3 bases are called codons

tRNA details (t = transfer RNA)

Found in cytoplasm

Single stranded but folded to create a leaf like shape and is held by H bonds

brings a specific amino acid to the ribosome

determine by the 3 bases on tRNA which is the anticodon and complementary to the 3 bases on the mRNA (codon)

Semi-Conservative DNA Replication

DNA replication is semi-conservative because each new DNA molecule contains:

• One original (parental) strand

• One newly synthesised strand

This ensures genetic information is passed accurately to daughter cells.

When Does Replication Occur?

• Takes place during the S phase of interphase in the cell cycle.

• DNA is copied before cell division

DNA Strand Direction

DNA strands have polarity:

5' (five-prime) end

• The phosphate group is attached to the 5th carbon of deoxyribose.

3' (three-prime) end

• The hydroxyl (-OH) group is attached to the 3rd carbon of deoxyribose.

• DNA polymerase can only add nucleotides to the 3' end.

• Therefore, new DNA is always synthesised in the 5' → 3' direction.

What is the function of helicase in DNA replication?

Helicase breaks the hydrogen bonds between complementary bases, unwinds the DNA double helix, and separates the two strands

What are single-stranded binding proteins (SSBs)?

Proteins that bind to separated DNA strands and prevent them from rejoining.

What is the role of DNA polymerase?

DNA polymerase adds complementary DNA nucleotides and forms phosphodiester bonds between them.

What is the function of DNA ligase?

DNA ligase joins DNA fragments together by forming phosphodiester bonds in the sugar-phosphate backbone. Joins Okazaki Fragments.

Leading Strand

• Synthesised continuously towards the replication fork.

• Requires only one RNA primer.

Lagging Strand

• Synthesised discontinuously away from the DNA

• Produced as short sections called Okazaki fragments.

• DNA ligase joins the fragments together.

Stages of DNA replications

.1- Unwinding DNA Helicase. Breaks hydrogen bonds between complementary base pairs. The double helix unwinds and the two strands separate into individual polymers.

2- Template Identification- Both separated strands serve as templates to ensure the genetic code is copied accurately for each new daughter molecule.

3. Complementary Base Pairing- Free-floating DNA nucleotides align opposite their complementary bases on the template strands. Hydrogen bonds reform between the specific base pairs (A-T and C-G).

4. DNA polymerase. Joins adjacent nucleotides together. Catalyst for the formation of phosphodiester bonds to create the new sugar-phosphate backbone.

The genetic code has 3 feature

Degenerate- Amino acid are coded for by more than one triplet of bases

Universal- Same triplet of bases code for same amino in all organisms

Non-Overlapping- Each base in a gene is only part of one triplet of bases that codes for one amino acid. Each codon or triplet read as a discrete unit.

What is Transcription

Where mRNA is created in nucleus

1- H bonds between bases breaks separating the strand

2- One DNA strand acts as a template

3- Free nucleotides align with complementary base pairs

4- In RNA Uracil used instead of thymine this uracil binds to adenine

5- Enzyme RNA Polymerase catalyses the condensation reaction of joining adjacent RNA nucleotide together

6- Phosphodiester bonds forming the sugar phosphate backbone

7- The once copied it leaves the nucleus to find a ribosome in the cytoplasm

What is translation

mRNA from transcription attaches to a ribosome at the start codon

• tRNA molecule with complementary anticodon align with mRNA. Ribosome can hold 2 tRNAs at a time.

• Amino acids delivered by tRNA joined via a Peptide bond formed between the catalysed byb an enzyme using ATP

• Ribosome move along to the next 3 bases and process repeats and continues until a stop codon where ribosome detaches

• Polypeptide chain now made and goes to the Golgi body to be modified

What are start and stop codons

Start codon enables the ribosome to attach

End codon causes ribosome to detach