Lecture 3 Biopolymers: DNA,RNA and proteins

What Are Biopolymers?

Biopolymers are long chains made by joining small building blocks.
During polymerisation, part of each monomer is lost, leaving a residue in the chain

They are formed by dehydration synthesis (water removed, energy required).

what is Nucleotides?

building block of DNA and RNA

Each nucleotide has:

• Phosphate (negatively charged)

• Sugar (ribose in RNA, deoxyribose in DNA)

• nucleoBase (A, G, C, T, U)

Purines: A, G
Pyrimidines: C, T, U

Purines have two rings; pyrimidines have one

DNA, RNA > can be long/short strand

what is Sugar‑Phosphate Backbone and characterisitcs, bodning

Nucleotides link via phosphodiester bonds:

• Phosphate attaches to 3′ carbon of one sugar above and 5′ carbon of the sugar below

This backbone is negatively charged and hydrophilic (sugar and phosphate).

direction of nucleic acid

Nucleic acids always run 5′ → 3′.

no of bond in AT CG and its impact on melting temp

• A = T (or A = U in RNA) → 2 H‑bonds

• G = C → 3 H‑bonds (stronger)

Higher GC content → higher melting temperature (Tm).

characterisitcs of Double‑Stranded DNA Structure

• Anti‑parallel strands (5′→3′ opposite 3′→5′)

• Bases stack flat inside helix

• Major and minor grooves form because of asymmetric geometry

  • Major groove: exposes more base information → proteins bind easily

  • Minor groove: narrower → fewer proteins bind

comparsion of DNA and RNA

DNA:

• Deoxyribose

• Double‑stranded

• Stable (can last thousands of years)

RNA:

• Ribose (extra OH group)

• Single‑stranded

• Unstable (mRNA lasts hours in cells)

• Can fold into structures (mRNA, tRNA, rRNA)

Cytosine can deaminate to uracil:

• DNA repairs U

• RNA does not (U is normal)

building block and repeating unit of protein

• Building blocks: amino acids

  • Amino group, carboxyl group, α‑carbon, R‑group

  • Polypeptide chains are the backbone of proteins

• Repeating unit: polypeptide backbone

  • Repeating N‑C‑C pattern

  • each amino acid in the chain will be differentiated by its R group

  • amino acid sidechain >varied property (non-polar, polar, hydrophobic, hydrophilic) >provide shape/structure/function to protein

key bond between amino acid in protein

• Key bond: peptide bond (formed by dehydration synthesis reactions)

  • very energetically unfavourable, doesn’t happen spontaneously

  • rigid, planar due to resonance

  • partial charges encourage hydrogen bonding

  • can still rotate around other bonds

how is amino acid categorized?

• Amino acids are categorized by their R-group properties:

  • non polar(hydrophobic) e.g. Alanine, Valine

  • polar (hydrophilic) e.g. Serine, Glutamine

  • Charged (acidic or basic) e.g. Aspartate (-), Lysine (+)

• charge of amino acid change depending on pH of thier solution( ionization state)

Direction of nucleic acid and protein

Nucleic acids

• Always written and synthesised 5′ → 3′ (in one direction only)

• DNA and RNA strands are anti‑parallel in double‑stranded DNA

Proteins

• Written and synthesised N (amino) ‑terminus → C (carboxy)‑terminus (in one direction only)

• Translation follows the RNA codon order to choose amino acids

type of RNA

mRNA, tRNA, rRNA

Describe how physical/chemical properties of nucleic acids are used experimentally

Nucleic acids Exploiting the sugar phosphate backbone for experimentation

• Negative charge → move toward positive electrode in electrophoresis

• Hydrophilic backbone → predictable solubility

• Application:

  • Ethanol precipitation

    • Salt neutralises charge → DNA/RNA becomes insoluble → precipitates

  • ELectrophoresis

• UV absorbance

  • Nucleic acids absorb at 260 nm

  • Purity ratios:

    • A260/A280 ≈ 1.8 → pure DNA

    • 2.0 → RNA contamination

    • <1.8 → protein contamination

    • A260/A230 >1.8 → pure nucleic acid

      • A260/A230 <1.8 → The sample may contain organic compound contamination

Describe how physical/chemical properties of proteins are used experimentally

Proteins

• Aromatic amino acids (Trp, Tyr, Phe) absorb at 280 nm

• Used to estimate protein concentration and detect contamination