Nucleic Acids and DNA Structure

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Questions and Answers

What are the two primary types of nucleic acids and what distinguishes their structure?

The two primary types of nucleic acids are DNA and RNA; DNA contains deoxyribose sugar and is usually double-stranded, while RNA contains ribose sugar and is typically single-stranded.

Describe Chargaff's Rule and its significance in DNA structure.

Chargaff's Rule states that the amounts of adenine (A) and thymine (T) are equal, as are the amounts of guanine (G) and cytosine (C); this is crucial for the complementary base pairing in the double helix structure of DNA.

What roles do the phosphate groups play in nucleic acids?

Phosphate groups provide the acidic properties of nucleic acids and form stable ester bonds that link nucleotides through phosphodiester bonds, establishing the backbone of DNA and RNA.

Differentiate between purines and pyrimidines in the context of DNA structure.

Purines, such as adenine (A) and guanine (G), have a double carbon-nitrogen ring structure, while pyrimidines, including thymine (T) and cytosine (C), have a single ring structure. Signup and view all the answers

What is the primary structure of DNA and how is it formed?

The primary structure of DNA refers to the linear sequence of nucleotides linked by strong phosphodiester bonds, consisting of deoxyribose sugar, phosphate groups, and nitrogenous bases. Signup and view all the answers

Explain how a nucleoside is formed from a base and sugar, and identify the chemical bond involved.

A nucleoside is formed by linking a base to a sugar at the 1′-carbon position, creating a glycosidic bond. Signup and view all the answers

Describe the significance of the 5′ and 3′ ends of a DNA strand.

The 5′ end has a phosphate group attached to the fifth carbon of the sugar, while the 3′ end has a hydroxyl group on the third carbon, determining the directionality of DNA synthesis. Signup and view all the answers

What role do hydrogen bonds play in the stability of DNA, and how many bonds are formed between adenine and thymine?

Hydrogen bonds provide structural stability to DNA by holding the strands together, with two hydrogen bonds formed between adenine and thymine. Signup and view all the answers

Discuss the concept of base stacking and its importance in nucleic acid stability.

Base stacking refers to the hydrophobic interactions between adjacent bases, which enhance nucleic acid stability by minimizing their exposure to water. Signup and view all the answers

Define major and minor grooves in DNA and explain their significance.

Major and minor grooves are the asymmetric spaces created by the sugar-phosphate backbone of DNA; they are significant for protein binding and site of interaction for regulatory proteins. Signup and view all the answers

Study Notes

Nucleic Acids

Long-chain polymers made of repeating units called nucleotides
Two types: DNA & RNA

DNA

Polymer of deoxyribonucleotides
Usually double-stranded
Found in chromosomes, mitochondria, and chloroplasts
Acts as genetic material in most organisms
Carries genetic information

DNA Structure

Primary structure: Linear sequence of nucleotides linked by phosphodiester bonds
Secondary structure: Double helix, stabilized by hydrogen bonds between bases & base stacking
Tertiary structure: Supercoiling

Primary DNA Structure

Deoxyribose: Sugar within each nucleotide
Bases: Nitrogen-containing molecules
- Purines: Adenine (A) & Guanine (G)
- Pyrimidines: Thymine (T) & Cytosine (C)
  - Thymine (T) unique to DNA, Uracil (U) unique to RNA
Phosphate Functional Group: Gives DNA its acidic properties

Chargaff's Rule

Number of Adenine (A) residues equals the number of Thymine (T) residues: [A] = [T]
Number of Guanine (G) residues equals the number of Cytosine (C) residues: [G] = [C]
Amount of purine bases equals the amount of pyrimidine bases: [A] + [G] = [T] + [C]

Nucleosides & Nucleotides

Nucleoside: Base + sugar (e.g., Adenine + Ribose = Adenosine)
Nucleotide: Base + sugar + phosphate(s) (e.g. Deoxyadenosine Monophosphate (dAMP))

5' and 3' Ends

5' end: Phosphate group attached to the 5' carbon of the sugar
3' end: Hydroxyl (OH) group attached to the 3' carbon of the sugar
DNA sequence written 5' end to the left, 3' end to the right
This is the direction of synthesis.

Secondary Structure of DNA

Hydrogen bonding:
- Adenine (A) pairs with Thymine (T) (2 hydrogen bonds)
- Guanine (G) pairs with Cytosine (C) (3 hydrogen bonds)
Base Stacking: Hydrophobic interaction between flat surfaces of adjacent bases, minimizes contact with water
- Involves Van der Waals forces
Major & Minor Grooves:
- Asymmetrical spacing between the sugar-phosphate backbones create major and minor grooves
- Major groove: Important for DNA-protein interactions (e.g., transcription factors)

Alternative Double-Helical Structures of DNA

B-DNA:
- Right-handed helix
- 10.5 bases per turn
- Found in most living organisms
A-DNA:
- Right-handed helix
- 11 bases per turn
- Occurs under low water content and high salt concentration
Z-DNA:
- Left-handed helix
- 12 base pairs per turn
- Found under high salt conditions, presence of alcohol, and methylated cytosines

Unusual DNA Secondary Structures

Slipped Structures: Occur in tandem repeats (e.g., 5'-TACGTACGTACGTACG-3')
Cruciform Structures: Short bubbles of unpaired single-stranded DNA formed by inverted repeats
Triple Helix DNA: Third DNA strand joins the first two strands, favoured by purine-pyrimidine stretches

Supercoiled DNA

Circular DNA with no free 5' or 3' ends
Exists in a twisted, three-dimensional structure
More energetically favorable than relaxed DNA
Topoisomerases relax supercoiled DNA

Topoisomerases

Enzymes that convert one topoisomer of DNA to another
Type I Topoisomerases: Relax supercoiled DNA by forming a transient single-stranded break
Type II Topoisomerases: Require ATP energy, form transient double-stranded breaks to pass another DNA helix through

RNA Structure

Typically single-stranded
Made of ribonucleotides linked by phosphodiester bonds
Ribonucleotide structure: Ribose sugar, one of four nitrogenous bases (A U G C), and a phosphate group
Less stable than DNA

Secondary & Tertiary RNA Structure

Stem and loop structure: Double-stranded regions with single-stranded loops
Internal loops: Single-stranded regions within double-stranded regions
Bulges: Single-stranded regions in a double-stranded stem
Junctions: Points where multiple stems meet

Types of RNA

Messenger RNA (mRNA):
- Carries the genetic code from DNA to ribosomes for protein synthesis
- 5' cap and 3' poly-A tail provide stability
Ribosomal RNA (rRNA):
- Major component of ribosomes
- Essential for protein synthesis
Transfer RNA (tRNA):
- Smallest type of RNA
- Transfers amino acids to the ribosome during protein synthesis
- Each amino acid has a specific tRNA

Other Types of RNA

Small Nuclear RNA (snRNA):
- Involved in splicing pre-mRNA into mature mRNA
Regulatory RNAs:
- microRNA (miRNA): Regulate gene expression by breaking down or blocking mRNA translation
- small interfering RNA (siRNA): Similar to miRNA , often produced from viral RNA
- antisense RNA (aRNA): Bind to mRNA and block its translation
Transfer-messenger RNA (tmRNA):
- Found in bacteria and plastids
- Tags proteins lacking stop codons for degradation, preventing ribosome stalling

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Description

Explore the fascinating world of nucleic acids, focusing specifically on DNA's structure and function. Learn about the components of DNA, including nucleotides, their arrangements, and the significance of Chargaff's Rule in genetics. This quiz will deepen your understanding of both DNA and RNA.