2.1.4 Nucleic acids

What are the differences between RNA and DNA nucleotides?

DNA:

• Adenine, Guanine, Cytosine, Thymine

• Deoxyribose sugar

• Phosphate group

RNA:

• adenine, guanine, cytosine, uracil

• ribose sugar

• Phosphate group

What’s a polymer

A large molecule made up of repeating smaller units called monomers

What’s the difference between purines and pryamidines

Purines = double ring structure

• adenine, guanine

Pyramidines = single ring structure

• cytosine, thymine, uracil

Where does condensation reactions occur

Between the phosphate group of 1 nucleotide and the pentose sugar of the next nucleotide. Condensation reactions join DNA/RNA nucleotides together to form DNA and RNA polynucleotides (polymers)

What type of bond forms between phosphate group and pentose sugar

Phosphodiester bonds

how is the sugar-phosphate backbone formed

the joining of many nucleotides via condensation reactions creates a chain of alternating phosphate groups and pentode sugars that create the sugar-phosphate backbone.

What does phosphorylated mean in the context of ADP and ATP

Phosphorylation is the addition of a phosphate group to an organic compound.

• ADP (adenosine diphosphate) = 2 phosphate groups

• ATP (adenosine triphosphate) = 3 phosphate groups

What’s the function of ADP and ATP

ADP:

• coenzyme that releases energy for metabolic processes

ATP:

• coenzyme that releases energy for metabolic processes

• Universal energy carrier - ATP from respiration is used to transfer energy in ever energy requiring process in cells

• Can be hydrolysed to form ADP and AMP

Structure of DNA

• made up of 2 polynucleotide strands that are anti parallel (5’ - 3’ and 3’ - 5’)

• 5’ - 3’ means the phosphodiester bonds will join the 5-carbon from one deoxyribose sugar to the phosphate group (of the same nucleotide) which in turn is joined to the 3-carbon of the deoxyribose sugar of the next nucleotide

• Arranged as a double helix

• found in the nucleus of eukaryotes in structures called chromosomes

• Polymer (made up of lots of DNA nucleotides)

• Hydrogen bonds between the nitrogenous bases of each strand (A-T = 2 H-bonds, G-C = 3 H-bonds) = complementary base pairing

Properties of DNA

1. stable molecule

   • the strong phosphodiester bonds provide strength

   • DNA is wrapped around specialised proteins = histones (forms histone coat)

2. Carries lots of information

   • 20 amino acids

3. Complementary base pairing

   • ensures the 2 polynucleotide strands have the same sequence of bases after DNA replication

   • passes information to mRNA for protein synthesis

4. Double helix

   • hydrogen bonds weak individually but strong together

5. Antiparallel strands

6. If 1 strand is damaged, the other acts as a template strand so information not lost

What are Chargaff’s rules

1. A purine always pairs with a pyramidine so the number of purines and pyramidines are equal

2. The relative numbers of the nitrogenous bases varies between species

Importance of hydrogen bonds

• hold the polynucleotide strands together

• Prevent unwinding of strands and strand separation

• Maintain 3D double helix structure

• Can be broken when needed I.e semi-conservative replication / transcription

• Only occurs between specific nitrogenous bases to prevent errors in semi conservative replication

How does semi conservative replication work

occurs in S phase of mitosis

• (eukaryotes only) histone coat is removed

• Enzyme DNA helicase unwinds the double helix and breaks the hydrogen bonds between the nitrogenous base pairs

• The ‘free’ DNA nucleotides are activated by the addition of 2 phosphate groups

• The activated dna-nucleotides are attracted to the exposed bases on each template strand.

• DNA polymerase (enzyme) catalyses the synthesis of 2 new polynucleotide chains by catalysing the condensation reactions between the deoxyribose sugar and phosphate group of adjacent nucleotides

• Hydrogen bonds form between the complementary base pairs

• DNA rewinds and histone coat is replaced

Roles of DNA helicase and DNA polymerase

• DNA helicase - unwinds and rewinds the double helix

• DNA polymerase - catalyses synthesis of 2 new polynucleotide chains and catalyses formation of sugar phosphate backbone

  • checks dna for errors

Importance of replication and conserving genetic information

• In SCR, there’s one original strand and one new strand. It’s important to retain an original strand to maximise accuracy, as each new strand is created from a template strand.

• We want to conserve genetic info to ensure genetic continuity between generations of cells as our body cells are replaced regularly, so we need new cells to carry out the same role as parent cells

Occurrence of random, spontaneous mutations

• Substitution - affects only 1 triple

  • not always have an effect as many triplets code for the same amino acid

• Deletion - removal of 1 or more bases - frame shift mutation as affects many triplets

• Insertion - addition of 1 or more bases - frame shift mutation as affects many triplets

Evidence for semi conservative replication

Meselson and Stahl:

• grew E-Coli bacteria with different isotopes of nitrogen (found in all bases)

• Nitrogen has 2 forms:

  • light = 14-N

  • Heavy = 15-N

• Bacteria exposed to 15-N so DNA became heavy

• Bacteria transferred to a medium with 14-N

• after 2 rounds of replication, DNA was centrifuges to compare the densities of isotopes

  • original DNA = only 15-N (dark band low in tube)

  • 1st gen = 14-N/15-N (lighter strand higher up tube)

  • 2nd gen = 14-N/15-N (same place as 1st gen) and 14-N/14-N (lighter + higher up)

DNA purification / more on mutations ??

Differences between RNA and DNA

DNA:

• deoxyribose sugar

• A, T, C, G

• Double stranded

• Consists of introns and exons

• Carries genetic information

RNA:

• ribose sugar

• A, U, G, C

• single stranded

• Different types of RNA

Types of RNA

• mRNA - Carries the genetic code from the DNA (same sequence of bases) to the ribosomes

  • single helix structure

• tRNA - carries the specific amino acids to the ribosomes according to its anticodon

  • single stranded clover leaf structure

• rRNA - forms the structure of the ribosome (+ proteins)

  • large subunit = joins amino acids together via PEPTIDE BONDS in translation

  • Small subunit = reads mRNA in translation

Each subunit has multiple rRNA molecules

Characteristics of the genetic code

• codon - sequence of 3 nucleotide bases (triplet code)

• Degenerate code - each amino acid can be coded for by more than one codon —>limits effect of mutations

  • 4³ = 64 different codons and only 20 amino acids

• Universal - one codon will code for the same amino acid in almost every organism

• Non-overlapping - each base is only read once in the codon it’s part of - each triplet is read separately

How do genes determine the structure of proteins?

• gene = a section of DNA that carries the instructions to code for a specific polypeptide chain

• genes determine the exact sequence that the amino acids join together - determines the structure and therefore function of protein

• Sequence of amino acids = primary structure of proteins

Protein synthesis - transcription

DNA —> mRNA (occurs in nucleus)

1. Part of DNA molecule unwinds (by DNA helicase), which breaks the hydrogen bonds between the complementary base pairs

2. exposed gene acts a template for freely floating RNA nucleotides that are attracted to the exposed bases.

3. RNA nucleotides do complementary base pairing whilst enzyme RNA polymerase creates the sugar-phosphate backbone of the mRNA molecule by joining the sugar-phosphate groups of each RNA nucleotide

4. When mRNA is complete and the gene has been transcribed, the mRNA will leave the nucleus via nuclear pores and heads to the ribosomes.

Protein synthesis: Translation

mRNA —> Protein (cytoplasm)

1. After leaving nucleus, mRNA attaches to a ribosome (Each ribosome contains rRNA)

2. in the cytoplasm, there’s free tRNA molecules that each have a triplet of unpaired bases at one end (anticodon) and an amino acid binding site on the other

3. tRNA molecules bind to their specific amino acids and bring them to the mRNA on the ribosome.

4. The anticodon on each tRNA pairs complementary with a codon on the mRNA

5. 2 tRNA molecules can fit onto one ribosome - each with an amino acid

6. condensation reactions join the 2 amino acids together via peptide bonds (this reaction is all catalysed by rRNA)

7. Process continues until a stop codon on the mRNA is reached - amino acid chain forms a polypeptide chain which folds to form a protein

EQ: explain what is meant by semi conservative replication

2 identical DNA molecules produced, each one made from 1 original strand and 1 new strand

Compare transcription in the prokaryotic cell with transcription in a human cell [6 marker]

Similarities:

• DNA acts as a template

• DNA helicase is used to unwind the DNA molecule

• RNA nucleotides (same as ribonucleotides) are attracted to exposed bases

• RNA polymerase forms phosphodiester bonds

Differences:

• takes place in the nucleus in humans, but in cytoplasm in prokaryotes

• prokaryotes have circular DNA, humans have linear

• transcription + translation occur simultaneously in pro, but not in humans

• mRNA must be spliced in humans but not pro

• human DNA is bound to histones but pro DNA isn’t

• humans form pre-mRNA but pro mRNA is already mature