DNA and RNA structures and roles

Structure of DNA

Each DNA molecule is a right-handed double helix made up of 2 anti parallel DNA polynucleotides held together by hydrogen bonds between complementary base-pairing between nitrogenous base pairs

Feature of DNA: consists of deoxyribonucleotides

A DNA polynucleotide strand is formed by joining deoxyribonucleotides (monomers) in a series of condensation reactions —> each containing a deoxyribose sugar, phosphate group, and nitrogenous base (A, T, C, G)

Feature of DNA: Sugar-phosphate backbone and nitrogenous bases

Deoxyribonucleotides in a strand are linked by phosphodiester bonds to form a sugar-phosphate backbone where

• negatively charged phosphate groups are outside the helix

• Hydrophobic interactions between stacked nitrogenous bases

• Hydrophobic nitrogenous bases within the core of the helix

Feature of DNA: Double helix structure

Right handed double helix consists of 2 single stranded anti parallel DNA polynucleotides wound around each other

1 chromosome made of 1 DNA molecule made of 2 DNA strands

Feature of DNA: Complementary base pairing

2 DNA strands are held together by hydrogen bonds between nitrogenous bases on opposite strands via hydrogen bonds (purine-pyramiding pairs, Chargaff’s rules)

Thus A and T & G and C will always be in 1:1 ratios

Adenine + thymine is 2 hydrogen bonds

Guanine + cytosine is 3 hydrogen bonds

PS: A and G are purines (2 carbon-nitrogen rings) while C, T, and U are pyrimidines (1 carbon-nitrogen ring)

PS: 1 complete turn of double helix is 10 base pairs, length of 3.4nm and 2nm wide

Feature of DNA: Antiparallel

2 DNA polynucleotide strands are antiparallel where each strand is oriented in opposite direction to each other, 5’ end with free phosphate group covalently bound to C5 of deoxyribose sugar and 3’ end with free hydroxyl group at C3 of sugar. VV —> directionality of a strand

Feature of DNA: Major and minor grooves in helix

Double helical shape gives rise to 2 unequally wide grooves—> they expose edges of nitrogenous bases to allow proteins like enzymes to interact with the bases.

Why are base pairing and hydrogen bonding important in DNA? (3)

1. DNA replication —> hydrogen bonding contributes to specificity for complementary base pairing to form double stranded DNA molecule —> specificity = each original can give rise to 2 identical structured and base sequence DNA copies to maintain genetic stability

2. DNA repair —> Mutations —> intact complementary strands can be used as templates to guide repair through hydrogen bonds vis complementary base pairing —> intact integrity of base sequences —> crucial for the DNA to function as hereditary material we do not want mutations

3. Stability of DNA molecules —> hydrogen bonds between nitrogenous base pairs (2 between A and T and 3 between G and C) + hydrophobic interactions between stacked bases + strong phosphodiester bonds holding adjacent nucleotides together (not easily broken)

Role of DNA (2)

• Serves as template for DNA replication and for transcription (both strands for replication, 1 strand for transcription)

• Codes for polypeptide chain (base sequence is derived from sequence of deoxyribonucleotides, 5’ to 3’ direction —> specific DNA base sequence —> codes for a specific polypeptide from amino acid sequence (3 bases) —> specifies protiens 3D conformation and thus function)

Suitability to role as information storage (3)

1. 4 different bases make up many possible gene sequences

2. 2 anti parallel strands protects base sequence within double helix and allows for DNA repair (templates)

3. Supercoiling takes up very little space within nucleus ( 2 strands = 1 molecule = 1 chromosome)

General structure of RNA

• Single stranded

• Not a long regular structure like DNA

• Ribonucleotides linked by phosphodiester bonds (like DNA)

• A, U, G, C (uracil)

• Forms globular conformations, regions of helical structure maintained by intramolecular hydrogen bonding and base stacking within a single nucleic acid strand formed when complementary parts

• Eg. hairpin loop when RNA folds, forming base pairs with another section of same strand

Types of RNA and their roles in translation (brief)

All 3 involved in translation —> gene sequence transcribed to mRNA in eukaryotic nucleus —> transported out from nuclear pore into cytoplasm —> ribosome (rRNA and proteins) bind to mRNA —> tRNA carries specific amino acid to ribosome and forms specific polypeptide chain

There are mRNA, rRNA, tRNA

Structures of all 3 RNA

mRNA is single stranded and exists as a random coil

rRNA has structural loops

tRNA is single stranded and folds in on itself to create a clover leaf structure by complementary base pairing via hydrogen bonds

• anticodon sequence complementary to codons on mRNA (determines sequence and position of amino acids on polypeptide chain)

• 3’ end has 5’-CCA-3’ sequence as an attachment site for amino acids

• 5’ end always ends with guanine

• At least 20 kinds one for each amino acid

• Shape complementary to active site of amino acetyl tRNA synthesase for amino acid activation

Synthesis of all 3 RNA

mRNA synthesised during transcription of DNA where base sequence is complementary to DNA template strand it was transcribed from

—> base sequence consists of codons (triplets of bases) each code for one amino acid

—> eukaryotes process mRNA to have

• 5’ modified guanine cap

• 3’ poly-A tail (AAAAAAAAAAAAAdenine)

• Exons ligated/joined together, introns excised

• 5’ and 3’ untranslated regions

rRNA synthesised during transcription of rRNA genes on nucleolus DNA

—> processed and assembled with proteins imported from cytoplasm to form ribosomal subunits —> exported via nuclear pores to cytoplasm for use in translation

tRNA synthesised during transcription of tRNA genes in nucleus —> must travel to cytoplasm for translation to occur

Roles of all 3 RNA

mRNA (messenger) conveys information from DNA in nucleus (eukaryotes) to synthesise proteins in cytoplasm

• template for translation (protein synthesis)

• Codons specify order and sequence in positioning amino acids to form a polypeptide

• Leaves nucleus via pore to cytoplasm where ribosomes bind to mature mRNA for translation and produce a polypeptide chain (specific amino acid sequence)

• Prokaryotes transcription and translation occur at the same time due to lack of nucleus

rRNA (ribosomal) —> Ribosomal subunits assemble with proteins to form ribosomes that hold mRNA and tRNA in close proximity to position new amino acid to growing polypeptide chain

• peptidyl transferase ENZYME ribozyme in large ribosomal subunit catalyse formation of peptide bond between amino acids during translation

tRNA (transfer) transports amino acids to ribosome for use in polypeptide / protein synthesis —> ensures correct position and sequence of each amino acid on elongating polypeptide chain

Similarities between DNA and RNA (3)

1. Both are polymers and polynucleotides made of repeating monomers

2. Nucleotides linked by phosphodiester bonds

3. Both have pentose sugar, phosphate group and nitrogenous bases (purines and pyrimidines)

Differences RNA and DNA (9)

1. Double stranded vs single stranded

2. Deoxyribose vs ribose Pentose sugar

3. Thymine vs uracil

4. 1:1 nitrogenous base ratios of Chargaff’s rule vs varying ratio

5. 1 basic form DNA vs 3 basic types (mRNA, rRNA, tRNA)

6. Found almost entirely in nucleus (excluding chloroplast and mitochondrion DNA) vs synthesised in nucleus but found throughout the cell

7. Synthesised via semi conservative DNA replication vs synthesised via transcription

8. Consistent amount for all cells in a species (excluding gametes and spores) vs varying amounts cell to cell depending on metabolic activity

9. Stable (double stranded, name all 3 types of bonds) vs less stable (single stranded —> easier for exonuclease to bind and break down