Molecular Biology: DNA and RNA Structure

Nucleic Acids

• Nucleic acids are organic molecules found in living organisms, primarily composed of Carbon, Hydrogen, Oxygen, and Nitrogen.
• Four major classes of biomolecules are lipids, proteins, carbohydrates, and nucleic acids.
• Nucleic acids are long biopolymers with structural similarities, serving as carriers of information, but with individual roles.
• DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid) are types of nucleic acids.

Learning Outcomes

• Understand the basic structure of a nucleotide.
• Outline the structure of the DNA double helix.
• Explain the structure and function of mRNA and tRNA for protein synthesis.
• Appreciate the role of the ribosome for protein translation.

Questions

• Students should use the provided TEAM platform for questions.
• Students should not consider questions silly.
• Emailed questions will be posted on the platform for the whole class to benefit from the answers.
• Anyone with the answer to a question can contribute, fostering collaborative learning.

Biomolecules

• A nucleoside consists of a base bonded to a sugar.
• A nucleotide combines a nucleoside with a phosphate group.

The Central Dogma

• DNA replicates to produce more DNA.
• DNA is transcribed into RNA (mRNA).
• mRNA undergoes translation into protein.

Nucleic Acids (Detailed)

• DNA is deoxyribonucleic acid.
• RNA is ribonucleic acid.
• Both are long biopolymers with structural similarities.
• Both carry information, but have individual roles.

Nucleic Acids as Polymers

• Nucleic acids are polymers formed from monomers called nucleotides.
• Nucleotides are composed of a nitrogenous base, a pentose sugar, and a phosphate group.

Nucleotide Structure

• Nucleotides contain a nitrogenous base, a pentose sugar (ribose or deoxyribose), and a phosphate group.

Sugar: Pentose-Ribose

• A five-carbon sugar, ribose, forms part of RNA's structure.

Sugar: RNA or DNA

• RNA uses ribose.
• DNA uses deoxyribose, differing by the presence of an oxygen atom on carbon 2.

Nitrogen Bases

• There are five nitrogenous bases in DNA and RNA.
• Two classes include pyrimidines and purines.

Bases: Purines

• Adenine (A) and Guanine (G) are purines, larger, double-ringed structures.

Bases: Pyrimidines

• Cytosine (C), Uracil (U), and Thymine (T) are pyrimidines (smaller, single-ringed structures).
• Uracil (U) is found in RNA; thymine (T) is in DNA.

Nucleosides and Nucleotides

• A nucleoside is a base bound to a sugar.
• A nucleotide is a nucleoside attached to a phosphate group on the 5' carbon.

Names of Nucleosides and Nucleotides

• Nucleosides and nucleotides have specific names based on the nitrogenous base (e.g., adenosine, cytidine).
• Nucleotides often have "5'-monophosphate" added to their names (e.g., adenosine 5'-monophosphate).
• Different names for DNA and RNA nucleosides/nucleotides reflecting the sugar (deoxy- prefix for DNA).

Bases

• The order of nitrogenous bases (A, T/U, C, G) dictates the genetic code.

DNA Structure

• DNA has a phosphate group at the 5' end and a hydroxyl group at the 3' end.
• DNA sequences are read from the 5' end.
• RNA, in contrast, has uracil (U) instead of thymine (T) and a ribose sugar instead of deoxyribose.

The DNA Double Helix

• DNA exists as a double helix.
• Two strands wind around each other, held together by hydrogen bonds between bases (A-T, C-G).
• The phosphate-sugar backbone is on the outside of the helix, with the bases inside.

Base-Pairing

• Hydrogen bonding between bases (A-T, G-C) holds the DNA strands together within the double helix.
• Purines pair with pyrimidines for proper base pairing.

Base Pairing in the DNA Double Helix

• Strands run antiparallel (3' to 5' and 5' to 3').
• Strands are described as complementary.
• Genetic information resides on one coded strand.
• Another strand acts as an anti-template.

Helix Dimensions

• Base pairs are 0.34 nm apart.
• A complete turn of the helix is 3.4 nm.
• Ten base pairs are found per turn.
• External diameter of the helix is 2 nm.

Grooves

• DNA has two grooves, major and minor, created by the twisting helix.
• Proteins interact with specific sites exposed in these grooves (e.g., transcription factors, repressors, and silencers).

DNA Denaturation

• DNA double strands can be separated by breaking hydrogen bonds (using changes in pH or heat).
• Phosphodiester bonds are not broken during denaturation.
• Temperature of melting (Tm) describes the temperature where 50% of the DNA becomes single-stranded.
• Higher Tm signifies a greater proportion of G-C base pairs, requiring more energy to break.

Double Helical DNA Denaturation

• DNA strands can be reversibly separated by extreme heat (above 80°C), changes in pH, and breaking hydrogen bonds.
• This process does not affect phosphodiester bonds.
• Renaturation restores the double helix.

The Genetic Code

• 64 codons, 61 for specific amino acids, and 3 for stop codons, describe the genetic code.
• There is redundancy since multiple codons can code for the same amino acid.

Codon Usage Bias

• Different organisms show variations in codon usage, favoring certain codons for specific amino acids.

RNA Synthesis & Function

• Synthesis of mRNA occurs in the nucleus from a DNA template.
• mRNA then translocates to the cytoplasm via nuclear pores for protein synthesis.

RNA Structure

• RNA is a single-stranded polymer of nucleotides.
• RNA employs ribose sugar and has bases A, G, C, and U.

Types of RNA

• Ribosomal RNA (rRNA) is largely involved in ribosome structure.
• Messenger RNA (mRNA) carries genetic information to direct protein synthesis.
• Transfer RNA (tRNA) delivers amino acids to the ribosome during translation.

RNA Messenger - mRNA

• mRNA is a copy of a DNA sequence (transcription).
• mRNA carries genetic information needed for protein synthesis.
• mRNA undergoes post-transcriptional modification.
• mRNA leaves the nucleus and travels to the cytoplasm, where proteins are produced.
• mRNA is a complementary copy of one DNA strand.

Ribosomal RNA - rRNA

• Ribosomes, where proteins are synthesized, are found in the cytoplasm.
• Ribosomes are composed primarily of rRNA (65%) and proteins (35%).
• They participate in binding mRNA, essential for proper protein translation.

Transfer RNA - tRNA

• tRNA transports amino acids to ribosomes during protein translation.
• Many types of tRNA exist, one for each amino acid.
• Each tRNA has an anticodon that complements an mRNA codon.

Protein Translation

• Protein synthesis occurs at ribosomes in the cytoplasm.
• mRNA, tRNA, and ribosomes collaborate for protein building, assembling amino acids as dictated by mRNA codons.

DNA Structure Review

• A single strand of DNA has a free phosphate group at the 5' end and a free hydroxyl group at the 3' end.
• The sequence moves from 5' to 3' ends, with bases indicating particular amino acid instructions.

Summary (Nucleic Acids)

• Nucleotides consist of a nitrogenous base, a pentose sugar, and a phosphate group.
• DNA and RNA have specific structures and functions related to encoding and translating genetic information.
• RNA and DNA have complementary sequences.

Further Reading

• Suggested sources for additional study are provided.

Explore the fundamental concepts of DNA and RNA structure through this quiz. You'll learn about the role of grooves, the double helix arrangement, and the differences between nucleic acids. Test your knowledge on nucleotides, ribosomes, and more in molecular biology.