nucleotides + nucleic acids

• Nucleotide


  Nitrogen containing monomer of nucleic acids made up of:

  - a pentose sugar (deoxyribose/ribose sugar)

  - a phosphate group (PO4 3-)

  - a nitrogenous base (AT CG/AU CG)
• Nucleic acids


  - large molecules made up of nucleotides joined together by phosphodiester bonds via condensation reactions

  - DNA and RNA
• DNA vs RNA


  Similarities:

  - both have a pentose sugar

  - both have a sugar-phosphate backbone

  - both have a phosphate group

  - both have A C and G in common

  - both are nucleic acids

  
  

  Differences:

  - DNA contains deoxyribose sugar but RNA contains ribose sugar

  - DNA had thymine (T) but RNA has uracil (U)

  - DNA is double stranded but RNA is single stranded
• Why do DNA and RNA have different roles?

  The presence of the 2 hydroxyl (OH) groups makes RNA more susceptible to hydrolysis so DNA is the storage molecule and RNA is the transport molecule with a shorter molecular lifespan
• Purines


  _ Bases with double ring structure

  - Can only form hydrogen bond with pyrimidines

  - Adenine (A)

  - Guanine (G)
• Pyrimidines


  Bases with a single-ring structure.

  - Thymine (T) / Uracil (U)

  - Cytosine (C)
• Adenine + Thymine


  2 H-bonds
• Cytosine + Guanine


  3 H-bonds

  
• Phosphodiester bond


  - Separate nucleotides are joined together via condensation reactions which occurs between:

  → a phosphate group of one nucleotide

  → OH group of pentose sugar of another nucleotide

  This forms a phosphodiester bond as there is one PO43- and two ester bonds

  
• Sugar-phosphate backbone


  The alternating chain of pentose sugar and phosphate as a result of many phosphodiester bonds to which nitrogenous bases are attached

  
• ATP


  - Nucleotide; Adenosine triphosphate

  - Universal energy currency

  
  

  Structure:

  - 3 phosphates, one ribose sugar and adenine

  - hydrolysed into ADP + Pi (inorganic phosphate) + 30.5kJ of energy

  
  

  Function:

  → Synthesis = formation of large molecules from smaller molecules (Anabolic reactions)

  → Transport = pumping molecules/ions in and out of membranes by active transport

  → Movement = muscle contraction requiring energy

  
• Properties of ATP


  - Releases energy in a small quantities so less is wasted as heat

  - Small, soluble molecule that can easily be transported around the cell

  - Easily broken down

  - Easily and quickly regenerated

  - Stays in cells - immediate energy source
• Structure of DNA


  - Double helix

  - Antiparallel = two polynucleotide strands side by side running in opposite directions

  - Complementary base pairs = bases joined by hydrogen bonds (A--T) (C---G)

  - purine always binds to pyrimidine

  - Phosphodiester bonds = Each DNA polynucleotide strand is made up of alternating deoxyribose sugars and phosphate groups bonded together to form the sugar-phosphate backbone
• 5' to 3'


  - The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the deoxyribose sugar molecule of the next nucleotide in the strand

  - Each DNA polynucleotide strand has 3' end and a 5' end

  - As the strands run in opposite directions (antiparallel), one is known as the 5' to 3' strand and the other is known as the 3' to 5' strand
• DNA replication


  1. Enzyme helicase unwinds/uncoils DNA double stranded helix

  → breaks the hydrogen bonds between complementary base pairs

  → forming two single DNA (polynucleotide) strands: each strands acts as a template to form new strands

  2. Free nucleotides from the cytoplasm (activated nucleotides with 3 phosphates) pair and assemble in complementary base pairs on the template DNA strands.

  → DNA polymerase adds bases in one direction (5' to 3')

  3. DNA polymerase catalyses condensation reactions between the deoxyribose sugar and phosphate groups of adjacent nucleotides within the new strands

  → creating new sugar-phosphate backbone of the new DNA strands

  → DNA polymerase cleaves (breaks off) the two extra phosphates and uses the energy released to create the phosphodiester bonds (between adjacent nucleotides)

  4. DNA polymerase joins bases of free nucleotides to the complementary bases of the original DNA strand with hydrogen bonds (hydrogen bonds reform)

  5. Two identical DNA molecules produced

  6. Each new DNA strand consists of one new strand and one old original strand = semiconservative replication
• Semi-conservative replication


  Each new DNA strand consists of one new strand and one old original strand

  
  

  IMP because:

  - Ensures genetic continuity (genes are conserved) so new cells produced during cell division inherit all their genes from their parent cells

  - As cells are replaced regularly, ensures that new cells carry out the same role as the old ones
• Continuous and discontinuous replication

  - DNA polymerase moves from 3' to 5'

  - The strand that is unzipped from 3' to 5' is the leading strand and can be continuously replicated as the strand unzips

  - The strand that is unzipped from 5' to 3' is the lagging strand and DNA polymerase has to wait until a section has unzipped to work back along the strand

  → DNA is produced in sections called Okazaki fragments

  → ligase enzymes joins the fragments together
• Mutations


  Random, spontaneous errors/ mutations

  - Bases being inserted into the complementary strand in the wrong order

  - An extra base being inserted by accident

  - A base being left out by accident
• Gene


  A section of DNA that codes for the sequence of amino acids of a polypeptide
• Genetic code


  The set of rules used by living organisms to translate information encoded within genetic material into proteins
• Four rules of the genetic code

  - Triplet = 1 amino acid is coded for by a sequence of 3 bases

  - Universal = same triplet code (aka codon) for the same amino acid in almost all organisms

  - Non-overlapping = each base is only part of one triplet

  - Degenerate = some amino acids are coded for by more than one base sequence as there are more base sequences (64) than amino acids (20)
• Start codon


  TAC → AUG

  Methionine
• Gene


  A sequence of nucleotide bases in a DNA molecule which codes for the production of a specific sequence of amino acids, which in turn make up a specific polypeptide chain (protein)
• Process of protein synthesis

  1) Transcription of DNA and formation of mRNA

  2) Translation of mRNA and produced of a sequence of amino acids
• Transcription


  Occurs in the nucleus

  1) Part of DNA double helix strand unwinds and unzips by DNA helicase

  → breaks down h bonds between complementary base pairs that hold the two strands together

  2) RNA polymerase binds to promoter region to initiate transcription

  → reads template strand from 3' to 5'

  3) Free RNA nucleotides bind to complementary bases on template (antisense) strand with h bonds by RNA polymerase, forming a complementary strand (mRNA): copy of DNA coding (sense) strand

  4) Phosphodiester bonds formed between ribose sugar and phosphate of adjacent RNA nucleotides, forming sugar-phosphate backbone by RNA polymerase

  5) RNA polymerase stops transcribing when it reaches the stop codon

  6) When transcription is complete and messenger RNA (mRNA) is formed (grows in 5' to 3' direction), h bonds between bases of mRNA and template strand of DNA are broken

  7) Double strand reforms and double helix rejoins

  8) mRNA leaves nucleus through nuclear pores
• Template strand


  Transcribed strand/Antisense strand

  - The strand of DNA on which free RNA nucleotides pair their bases up with and form h-bonds with temporarily until mRNA has formed

  - Used to produce mRNA

  - Has complementary (opposite) bases to mRNA = ANTIsense
• Coding strand


  Non-transcribed/Sense strand

  - Strand of DNA that has same bases as mRNA (except mRNA has uracil (U) instead of thymine (T)
• Stop codon


  - A triplet that does not code for amino acids

  - Signals end of transcription
• Structure of ribosomes


  - Made of rRNA and proteins

  - 2 subunits of rRNA

  → big subunit = contains peptidyl transferase which catalyses the condensation of amino acids

  → small subunit = binds to codon of mRNA (start codon = AUG so anticodon = UAC)
• Structure of transfer (t)RNA

  - Clover shape

  - at the top there is a binding site for amino acids

  - at the bottom there is the anticodon which is complementary to start codon of mRNA
• Translation


  Occurs in cytoplasm

  1) mRNA attaches to ribosome that is made up of two subunits of rRNA (small subunit of ribosomes binds to mRNA) and moves in 5' to 3' direction

  2) tRNA bind to their specific amino acid also binds to start codon of mRNA AUG (on the ribosome) by forming h bonds between start codon and tRNA's anticodon UAC as their bases are complementary

  3) two tRNA molecules can fit onto one ribosome

  4) Peptidyl transferase (and ATP) catalyse condensation reaction between the 2 amino acids forming a peptide bond (specific primary structure = specific order of amino acids) > then gives rise to secondary and complex 3D tertiary structure

  5) Empty tRNA released to collect another amino acid it codes for

  6) This is repeated until stop codon is reached to end translation

  7) Polypeptide chain (protein) formed

  
  

  *Many ribosomes can travel along the mRNA at the same time = polysome
• PAG 9: DNA extraction and purification

  1) Crush strawberries using a pestle and mortar

  → helps break down cellulose cell wall

  → easier to break down cells to release DNA

  2) Add detergent to water and add strawberries

  3) Put in water bath

  → detergent and heat will disrupt the phospholipid bilayer

  → heat denatures enzymes that would otherwise digest the DNA

  → dissolve/ break down CSM (plasma membrane) and nuclear membrane

  → DNA released

  4) Add protease enzyme (found in pineapple juice)

  → breaks down histones.proteins associated with DNA

  5) Using the filter paper, filter the mixture into another beaker

  → removes cell debris and membrane fragments

  → filtrate now contains the DNA and its associated proteins

  6) Add salt to solution

  → neutralises the negative charges on the DNA and thus enables the DNA strands to stick and clump together

  7) Add ice cold ethanol

  → DNA forms a precipitate (white layer) as it is insoluble in ethanol (soluble in water) so should float on the top