2.3 Nucleic Acids

Structure of a nucleotide

• Monomers from which DNA and RNA polymers are made

• Contain

  • Pentose sugar

  • Nitrogenous base

  • Phosphate group

DNA vs RNA

• DNA

  • Deoxyribose sugar

    • Contains one fewer oxygen than ribose

    • Carbon 2 has an H group

  • Four bases

    • Adenine

    • Cytosine

    • Guanine

    • Thymine

  • Double stranded

• RNA

  • Ribose sugar

    • Carbon 2 has an OH group

  • Four bases

    • Adenine

    • Cytosine

    • Guanine

    • Uracil

  • Single stranded

Purines

• Double ring structure

• Adenine and guanine

• PURE LAG (purines, long, a and g)

Pyrimidines

• Single ring structure

• Cytosine, thymine and uracil

Phosphodiester bond

• Bond that joins monomers of nucleotides together to form polymers of DNA and RNA

  • Joined via condensation reaction between phosphate group of one nucleotide and pentose sugar of next

• Alternating pattern

  • Phosphate group and pentose group creates a sugar-phosphate backbone

DNA structure

• Is made from two polynucleotide strands

  • Are antiparallel as they run in opposite directions

  • Double helix

• Made of alternating deoxyribose sugars and phosphate groups

  • Form sugar-phosphate backbone

  • Covalent bonds known as phosphodiester bonds

    • 5-carbon and 3-carbon

Hydrogen bonding

• Holds strands together between nitrogenous bases

  • A - T (two hydrogen bonds)

  • C - G (three hydrogen bonds)

• Complementary base pairing

Double helix

• Three dimensional shape formed by twisting of molecule

• Wound around histones (proteins)

• Seen by x-ray diffraction

Energy

• All organisms require energy

  • For anabolic reactions

  • For moving substances

• In animals

  • For muscle contractions

  • Conduction of nervous impulses

ATP

• From respiration

• Is used to transfer energy in all energy-requiring processes in cells

• This is why it is known as universal energy currency

• Is a nucleotide

ATP structure

• The energy carrying molecule

• Is a type of nucleic acid so its structurally similar to nucleotides of DNA and RNA

• Structure

  • Contains adenine (a nitrogenous base)

  • A pentose sugar (ribose)

  • 3 phosphate groups

    • One is AMP

    • Two is ADP

    • Three is ATP

• Condensation and hydrolysis reactions

Properties of ATP

• Hydrolysis of ATP releases small amounts of energy

  • Little energy is lost as heat

• Is broken down in one step so energy is released quick

• Can rapidly resynthesise

  • Always readily available

• Soluble

  • Easily transported

• Bonds between phosphate groups are unstable

  • Low activation energy and easily broken

DNA replication

• Semi-conservative

  • Produces DNA molecules of one original DNA strand and one newly synthesised DNA strand

Process of DNA replication

• Helicase breaks hydrogen bonds between complementary bases

• This unwinds the double helix and separates the strands

• Each strand acts as a template as free nucleotides attract their complementary bases

• DNA polymerase joins to free nucleotides together via condensation

  • In 5' to 3' directions

  • Forms phosphodiester bonds to create sugar-phosphate backbone

• Two identical copies of DNA are made

  • Each made from one of original DNA strand

Conservative vs semi-conservative replication

• Conservative

  • DNA molecules stay intact while new copy is built

  • After replication, one molecule has OG strand and the other has two new strands

• Semi-conservative

  • Original DNA splits and each strand acts as template

Meselson-Stahl experiment

1. Bacteria were grown in medium containing N15 (DNA is heavy)

2. Bacteria were transferred to a medium with N14 for one round of replication

   • Lighter nitrogen was incorporated in any new strands of DNA made

3. Centrifuged the DNA which was extracted

4. Steps 2-3 repeated

5. Distribution was analysed to see how DNA was replicating

   1. Heavier strands sunk to bottom

   2. Intermediate (one strand of heavy, one of light)were in middle

   3. Lighter at the top

Results of Meselson-Stahl Experiment

• Parent generation

  • All heavy DNA

• First replication

  • Original heavy strands separate

  • Each heavy strand acts as a template for new strand

  • Results in DNA molecule with one strand heavy and one light

  • Means all intermediate

• Second generation

  • Both original strands and new strands act as templates

  • New light strands form complementary to all four templates

  • Means half are intermediate (mix of N15 and N14) and other half are light

What is DNA purification

• Precipitation reaction to purify DNA

• Marmur preparation (method used)

  • Consists of

    • Lysing the cell and disrupting the nuclear membranes to release DNA

    • Using enzymes to denature and remove the histones

    • Precipitating the DNA

DNA purification pt1 steps

• Cut up onion into small pieces

• Add washing-up liquid to 90cm3 of tap water in beaker

• Add onions to beaker

 

• Place beaker into water bath as 60C for 15 minutes

  • Detergent and heat disrupt phospholipid bilayer

    • Releases DNA

  • Heat denatures enzymes released from cell that would have digested DNA

 

• Cool mixture in ice-water bath for 5 mins

  • Lowers temperature

    • Prevents DNA from breaking down

  • Continual stirring

    • Evenly distributes heat

DNA purification pt2 steps

• Blend mixture in blender for 5 seconds

  • Breaks down cell wall

  • Only for short amount of time so that DNA does not get broken apart

 

• Using filter paper, filter the mixture into another beaker

  • Removes cell debris and membrane fragments

  • Leaves on DNA and histones

 

• Pour filtrate into test tube and add 2-3 drops of protease

  • Denatures and removes the proteins

    • Leaves just DNA

 

• Add ice-cold ethanol to test tube

  • Nucleic acids are insoluble in ice-cold ethanol

  • DNA forms a precipitate

Genetic code structure

• DNA is wound around histones

• They get condensed to form chromatin which helps pack DNA into chromosomes

Genes

• Section of DNA that codes for a protein

• Each is located at specific position along a chromosome called a locus

Genetic code is: universal, degenerate, non-overlapping

• Universal

  • Each DNA triplet codes for the same amino acid in all organisms

• Degenerate

  • Most amino acids are coded for by more than one triplet

• Non-overlapping

  • Each base in DNA sequence is only read once

mRNA

• Messenger RNA

• Features

  • Single stranded

  • Contains base sequence complementary to DNA

  • Contains codons (base triplets)

  • Small

  • Longer than tRNA

tRNA

• Transfer RNA used in translation

• Features

  • Single stranded folded into clover-leaf

  • Uses hydrogen bonds to hold it in shape

  • Has anticodon

  • Contains an amino acid binding site at the opposite end

Transcription

• RNA polymerase binds to DNA in nucleus

• Hydrogen bonds between complementary bases break

  • Two strands separate

• Antisense strand acts as template

• Free RNA nucleotides align with DNA template with complementary base pairing

  • U pairs with A, A pairs with T, C pairs with G

• RNA polymerase catalyses formation of phosphodiester bonds

• mRNA strand is formed and complementary

• Process ends when RNA polymerase reaches stop codon

• DNA rewinds and mRNA leaves via nuclear pore

Translation

• Ribosome attaches to mRNA at start codon

• A tRNA molecules with complimentary anticodon to codon binds to mRNA

• Second tRNA molecule binds to next with specific amino acid

• Amino acid carried by first two tRNA molecules link via peptide bond

• First tRNA molecule detaches from mRNA

• Ribosome moves along mRNA in codons and allows another tRNA molecule to bind to next mRNA

• Polypeptide chain is made from amino acids

• Sequence continues until ribosome reaches stop codon on mRNA

• Polypeptide detaches and folds up