LO: Describe the structure and function of nucleic acids (DNA and RNA)

Nucleic acids

Deoxyribonucleic acid (DNA)

• 10% of cellular nucleic acid content
• Template for synthesis of RNA (then enables protein synthesis) and DNA (DNA replication)
• Storage and inheritance of genetic information

Ribonucleic acid (RNA)

• Ribosomal (rRNA) - structural and functional roles in ribosomes
• Messenger (mRNA) - carry genetic information from nucleus to cytoplasm, template for translation
• Transfer (tRNA) - translates genetic information by delivering amino acids to mRNA in the right order in protein synthesis

Nucleotides

• Building blocks (monomers) of nucleic acids
• Phosphate group
• Nitogenous base
• Pentose (5C) sugar
• Base + sugar = nucleoside
• Nucleoside + phosphate = nucleotide

Nitogenous bases

Pyrimidines

• Single nitrogen-containing ring
• Cytosine (C, DNA and RNA)
• Thymine (T, DNA)
• Uracil (U, RNA)

Purines

• Two nitrogen-containing rings
• Adenine (A) and Guanine (G)

Nucleotide functions

Adenosine triphosphate (ATP) and adenosine diphosphate (ADP)

• Cellular energy currency
• cyclic adenosine monophosphate (cAMP) is a chemical messenger in cell signalling

Guanosine triphosphate (GTP) and guanosine diphosphate (GDP)

• Energy currency in few reactions
• Messenger inside cells

Primary structure of DNA

• Nucleotides join together to form a sugar-phosphate backbone
• Phosphate on Carbon 5 bonds to OH on Carbon 3 on next nucleotide
• Phosphodiester bond
• Purine bases form hydrogen bonds with pyrimidine bases (Watson Crick base pairing)
• A with T (2 hydrogen bonds)
• G with C (3 hydrogen bonds)
• Two single stranded DNA wind around each other to form a double stranded DNA helix (double helix)
• Sequence of bases determines the genetic code and order of amino acids in proteins

RNA structure

• Generally single stranded
• U instead of T
• Extensive secondary structure, folds into shapes depending on nucleotide sequence

DNA replication

• Ensures genome is maintained when cells divide
• Occurs in S phase of cell cycle, before mitosis and G2
• Growth and development
• Repair
• Reproduction, needed in meiosis
• Semi-conservative: one of the old strands is always conserved in new DNA molecule

Stages

• Initiation - helix unwinds
• Elongation - complementary base pairing elongates the new copy
• Termination - joining of fragments in the chain

1. Each strand acts as a template strand for new strands
2. DNA unwound by DNA helicase, enzyme that breaks hydrogen bonds between paired bases
3. Unwinding starts at several points along DNA, replication forks
4. DNA primase makes temporary RNA primer at origins of replication
5. DNA polymerase adds nucleotides with bases complementary to template to 3' end
6. DNA polymerase proofreads the added bases and removes incorrect ones via exonuclease activity
7. DNA ligase joins Okazaki fragments

• New strands are only made in the 5' to 3' direction due to shape of polymerase
• Leading strand: continuously made as polymerase is in the direction of winding
• Lagging strand: polymerase in the opposite direction of winding, so not continuous. Polymerase makes repeated short fragments of DNA (Okazaki fragments) from RNA primers and replaces them with DNA

'Central dogma' of molecular biology

• Genetic information only flows in one direction from DNA-RNA-protein
• There are several exceptions
• RNA viruses - RNA-proteins
• Retroviruses - RNA-DNA-RNA-proteins
• Prions - proteins

Transcription

• Making mRNA in the nucleus
• mRNA - complementary copy of a section of DNA
• Initiation
• Elongation
• Termination
• RNA processing

1. RNA polymerase attaches to promotor region, section of DNA that defines the start of a gene and which strand is transcribed
2. RNA polymerase unzips segment of helix, initiates RNA synthesis which requires no primer
3. RNA polymerase moves along template strand and adds RNA nucleotides to 3' end and are complementary to the DNA nucleotides
4. Elongation of mRNA continues until RNA polymerase reaches a termination sequence, stops transcription and release the mRNA

• DNA is double stranded but only one strand is transcribed
• Template strand - 'non-coding' strand as does not have the same sequence as mRNA
• Non-template strand - 'coding' strand as it matches the mRNA (U $\rightleftharpoons$ T)

Translation

• DNA nucleotide sequence specifies the order of amino acids in polypeptide chain, central dogma of molecular biology
• mRNA sequences of 3 nucleotides makes a codon that codes for an amino acid
• 64 different codons (4! = 4x3x2x1 = 64) but only 20 naturally occurring amino acids
• Code is degenerate as different codons can code for the same amino acid, which reduces the chance that a mutation affects protein function
• Start codon: AUG
• Stop codons: UAA, UAG, UGA

Ribosomes

• "Read" the code of mRNA and translates to a sequence of amino acids
• Ribosomes are made of two subunits (large and small) composed of rRNA and protein
• Bacterial ribosomes are different which allows antibiotics to bind
• 3 sites for tRNAs to bind: A, P and E sites

tRNA

• Bind to mRNA codons via anticodons
• Other end (3') binds to an amino acid
• Different tRNAs carry different amino acids
• Aminoacyl-tRNA-synthetases load tRNAs with their corresponding amino acids

Process

1. mRNA travels to cytoplasm, mediated by carrier proteins and enzymes
2. Small ribosomal subunit binds to start of mRNA and scans to find start codon
3. tRNA carrying methionine attaches to start codon of mRNA
4. Large ribosomal subunit joins to form the initiation complex, which has the methionine-tRNA in P site
5. tRNA with anticodon matching next mRNA arrives at A site
6. Methionine detaches from tRNA and forms a peptide bond with amino acid at A site
7. Ribosome moves along by one codon moving empty tRNA molecule to E site and A site tRNA to P site
8. Third tRNA binds to codon at vacant A site and this continues
9. At stop codon, this does not code for a tRNA or amino acid. A release factor binds and breaks the last tRNA-polypeptide bond which releases the polypeptide away from ribosome