6. Nucleic Acids

MIT OpenCourseWare

12 May 202048:54

EducationalLearning

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TLDRThis lecture reviews the structure of nucleotides - the building blocks of nucleic acids like DNA and RNA. It examines the components of nucleotides: pentose sugars (ribose and deoxyribose), phosphate groups, and nitrogenous bases (purines and pyrimidines). It then shows how these components link together to form nucleic acid polymers. A key focus is understanding the hydrogen bonding between complementary bases, which gives DNA its double helical structure. The lecture concludes by contrasting DNA versus RNA and highlighting new research into using DNA for nanoscale computing and information storage.

Takeaways

😀 Nucleotides are the building blocks of nucleic acids like DNA and RNA. They consist of a sugar, a phosphate group, and a nucleobase.
👨‍🔬 DNA and RNA have slightly different structures - DNA contains deoxyribose while RNA contains ribose sugar.
🧬 DNA usually occurs as a double helix consisting of two antiparallel polynucleotide strands stabilized by hydrogen bonds.
🔬 Rosalind Franklin's X-ray diffraction data provided key insights into the structure of DNA.
💡 Chargaff's rules state that in DNA, the amount of adenine equals thymine and guanine equals cytosine.
🔬 Complementary base pairing between purines and pyrimidines stabilizes the DNA double helix structure.
👓 The major difference between DNA and RNA is that RNA contains uracil instead of thymine.
⚛️ DNA and RNA consist of a phosphodiester backbone with protruding nucleobases.
🔬 DNA replication occurs in a 5' to 3' direction by adding nucleotides to the 3' end.
🧪 There is interest in using DNA for applications like information storage and computing due to its predictable base pairing properties.

Q & A

What is the key difference between DNA and RNA sugars?
-The key difference is that DNA contains deoxyribose sugar which has no OH group on the 2' carbon, while RNA contains ribose sugar which has an OH group on the 2' carbon. This small difference makes DNA more stable than RNA.
Why is the antiparallel orientation of DNA strands thermodynamically favored?
-The antiparallel orientation allows for optimum base pairing and hydrogen bonding interactions between the strands, making it more stable. Attempts to pair the strands in parallel orientation result in poor hydrogen bonding and instability.
How did Rosalind Franklin's data help reveal the structure of DNA?
-Rosalind Franklin's X-ray diffraction data provided measurements of the spacing between DNA strands. This critical dimension, along with Chargaff's base pairing ratios, allowed Watson and Crick to deduce the double helix structure.
What is the significance of the DNA backbone being acidic?
-The acidic phosphate groups along the backbone give DNA an overall negative charge. This charge aids stability by promoting counterion accumulation to dampen electrostatic repulsion.
What is DNA origami?
-DNA origami involves deliberately designing DNA sequences that will self-assemble into predetermined 2D and 3D shapes through specific base pairing interactions. Complex nanostructures have been created using this technique.
What does Chargaff's ratio state about DNA bases?
-Chargaff found that across all organisms, DNA maintains a one-to-one ratio between purine and pyrimidine bases. This suggested that purines pair specifically with pyrimidines.
Why is DNA more stable than RNA?
-DNA's deoxyribose sugar and base-paired double helix structure make it very stable compared to the more reactive ribose found in single-stranded RNA regions.
How many hydrogen bonds can form between guanine and cytosine base pairs?
-Guanine can form 3 hydrogen bonds with cytosine. In contrast, adenine and thymine can only form 2 hydrogen bonds per pair.
What is the convention for naming directions in nucleic acid sequences?
-By convention, nucleic acid sequences are always written from the 5' end to the 3' end to reflect the directionality of linkage between phosphate groups.
What is cyclic AMP and what is its function?
-Cyclic AMP is a small signaling molecule made from adenosine triphosphate (ATP). It acts as a "second messenger" to regulate various cellular processes in response to extracellular signals.

Outlines

00:00

📚 Overview of lecture topics and importance of nucleic acids

This paragraph overviews the lecture topics, emphasizing how pivotal and essential nucleic acids are for programming protein biosynthesis and regulation. It highlights DNA's role in information storage and transfer and introduces different forms of RNA and nucleotides like mRNA, rRNA, tRNA, ATP, GTP, and cAMP.

05:03

🍬 Key components and structures of nucleotides

This paragraph details the key components of nucleotides: pentose sugars (ribose and deoxyribose), phosphate groups, and nitrogenous bases (purines and pyrimidines). It explains the numbering and nomenclature systems used to describe these components and nucleic acid sequences.

10:05

🧬 Examples of nucleotides important for cell signaling

This paragraph gives examples of some biologically important nucleotides other than the DNA/RNA bases that serve signaling functions: ATP, GTP (used for energy transfer), and cAMP (cyclic AMP, a second messenger)

15:05

📜 More on nucleosides, nucleotides and nucleic acid polymers

This paragraph further clarifies terminology related to nucleotides, contrasting nucleosides and nucleotides. It also overviews how nucleic acid polymers like DNA are formed through phosphodiester linkages between nucleotides in a condensation reaction.

20:10

🚦 Key structural features of the DNA double helix

This paragraph details key structural features of DNA: the phosphodiester backbone, the 5' to 3' directionality, the base pairing between purines and pyrimidines, and the convention for writing nucleic acid sequences in the 5' to 3' direction.

25:10

🔬 Experiments leading to elucidation of DNA structure

This paragraph recounts the historical experiments that were critical for deducing DNA's double helical structure - Chargaff's rules establishing the 1:1 ratio between purines and pyrimidines, and Rosalind Franklin's X-ray diffraction data.

30:11

👫 Base pairing explains Chargaff's ratio and DNA structure

This paragraph shows how the specific base pairing interactions between purines and pyrimidines explains Chargaff's ratio and clarifies important features like the antiparallel orientation of the DNA strands.

35:11

🤝 Comparing and contrasting key features of DNA and RNA

This paragraph highlights key differences between DNA and RNA like the deoxyribose vs. ribose sugar, higher stability of DNA vs. transience of RNA, predominant double stranded nature of DNA vs. diverse roles and shapes adopted by various RNAs.

40:14

🔎 Using base pairing rules to analyze DNA stability

This paragraph examines DNA base pairing patterns to illustrate factors that contribute to double helix stability, including GC content and hydrophobic interactions between stacked bases.

45:14

💻 DNA as an information storage material in nanoscale computing

This closing paragraph notes exciting applications of DNA in nanoscale computing, information storage, and programmable self-assembly of origami shapes - additional details are beyond the scope but can be explored independently.

Mindmap

Keywords

💡Nucleotides

Nucleotides are the building blocks of DNA and RNA. They consist of a nucleobase, a 5-carbon sugar (ribose or deoxyribose), and phosphate groups. Understanding the structure of nucleotides is critical for understanding nucleic acids. The video focuses extensively on the components of nucleotides and how they come together to form DNA and RNA.

💡DNA

DNA (deoxyribonucleic acid) is one of the two major types of nucleic acids, consisting of nucleotides with deoxyribose as the sugar component. DNA stores genetic information in its sequence of nucleotide bases. A key theme of the video is understanding DNA structure to explain how it can store and transfer biological information.

💡RNA

RNA (ribonucleic acid) is the other major type of nucleic acid, consisting of nucleotides with the ribose sugar. RNA plays important roles in protein synthesis and regulation. The video contrasts RNA and DNA structures to highlight key differences related to their distinct functions.

💡Base pairing

Base pairing refers to the specific pairwise hydrogen bonding between nucleotide bases that holds together the two strands of DNA. The video explains Chargaff's rules and base complementarity to illustrate how base pairing enables storage of genetic information.

💡Double helix

The term refers to the spiral staircase-like structure of DNA, consisting of two complementary antiparallel strands base paired through hydrogen bonds. Understanding this structure was pivotal for elucidating how DNA stores information.

💡Replication

Replication is the process of making an identical copy of DNA prior to cell division. The video notes that the antiparallel structure of DNA strands is important for the process of replication from parent to daughter DNA strands.

💡Transcription

Transcription is the process of synthesizing RNA from a DNA template. This relates to the central dogma shown in the video - the flow of genetic information from DNA to RNA to protein.

💡Translation

Translation refers to the process by which the nucleotide sequence of RNA directs the assembly of amino acids into protein sequences. This is another part of the central dogma relating DNA/RNA to protein synthesis.

💡Mutation

A mutation is a change in the nucleotide sequence of DNA. The video mentions glycosidases that can cleave mutated DNA to prevent errors in information encoding.

💡DNA computing

An emerging field using DNA as programmable, nanoscale building blocks for information storage and computing. The video highlights the potential of DNA base pairing for computational logic and assembly into defined structures.

Highlights

Nucleotides are key building blocks for DNA and RNA that store and transfer genetic information

DNA structure is a double helix of antiparallel strands with complementary base pairing between purines and pyrimidines

Chargaff's rules show a 1:1 ratio between purines and pyrimidines, suggesting base pairing in DNA structure

Rosalind Franklin's X-ray diffraction data provided key spacing dimensions of the DNA double helix

The difference between ribose and deoxyribose sugars impacts stability of RNA vs DNA polymers

DNA replication occurs by separating antiparallel strands and using them as templates to synthesize new complementary strands

DNA base pairing patterns and stacking interactions contribute to stability of the double helix structure

DNA can be manipulated to create complex nanoscale shapes and structures through base pairing interactions

DNA computing aims to leverage the programmability of DNA base pairing for applications like information storage and logic gates

Adenosine triphosphate (ATP) and guanosine triphosphate (GTP) serve as energy carriers in metabolic processes

Cyclic AMP acts as an important second messenger for signaling within cells

DNA sequence is always written 5' to 3' by convention to match direction of synthesis

RNA forms more structural varieties than DNA due to differences like the 2' OH group on ribose

Chargaff's rules suggested a base pairing pattern between purines and pyrimidines

Pauling's incorrect DNA model failed due to too much charge repulsion from excess phosphates

Transcripts

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