Chapter 1: Nucleic Acid Structure and Gene Expression

Types of RNA Molecules: An Overview

RNA molecules can be divided into two broad classes: coding RNA and noncoding RNA.

Messenger RNA (mRNA): Function: Carries genetic information from DNA to the protein synthesis machinery. Location: mRNA made in the nucleus is exported to the cytoplasm for protein synthesis. mRNA synthesized in mitochondria and chloroplasts is used within these organelles. Role: Essential for gene expression, as it translates genetic information into polypeptides, making proteins the major functional endpoint of DNA information.

Noncoding RNA: Function: Does not serve as a template for polypeptide synthesis. Role: Assists in gene expression regulation, either generally or by targeting specific genes. This includes catalytic RNA molecules known as ribozymes.

Most genetic information fl ows in the sequence DNA -> RNA -> polypeptide

Two processes are essential in all cellular organisms: • transcription, by which DNA is used by an RNA polymerase as a template for synthesizing one of many different types of RNA; • translation, by which mRNA is decoded to make polypeptides at ribosomes, which are large RNA–protein complexes found in the cytoplasm, and also in mitochondria and chloroplasts.

Genetic information is encoded in the linear sequence of nucleotides in DNA and is decoded in groups of three nucleotides at a time (triplets) to give a linear sequence of nucleotides in RNA. This is in turn decoded in groups of three nucleotides (codons) to generate a linear sequence of amino acids in the polypeptide product.

(A) The linear backbone of nucleic acids consists of alternating phosphate and sugar residues. Attached to each sugar is a base. The basic repeat unit (pale peach shading) consists of a base + sugar + phosphate = a nucleotide. The sugar has fi ve carbon atoms numbered 1¢ to 5¢. (B) In DNA, the sugar is deoxyribose. (C) In RNA, the sugar is ribose, which diff ers from deoxyribose in having a hydroxyl (OH) group attached to carbon 2¢.

Sure! Here’s a comprehensive, detailed set of notes on Nucleic Acid Structure and DNA Replication that also incorporates terminologies, diagrams, and essential concepts, enhanced for depth and clarity:

Nucleic Acid Structure and DNA Replication

Overview

Nucleic acids, DNA and RNA, are polymers of nucleotides. They consist of a sugar-phosphate backbone and nitrogenous bases, which carry genetic information.

Structure of DNA and RNA

1. Backbone of Nucleic Acids:

   • DNA and RNA have a linear backbone consisting of alternating sugar residues and phosphate groups.
   • The sugar residues are linked by 3’, 5’-phosphodiester bonds, where a phosphate group links the 3’ carbon atom of one sugar to the 5’ carbon atom of the next sugar in the backbone.

2. Double Helix Structure of DNA:

   • DNA exists as a double-stranded molecule, where two complementary strands run in antiparallel orientation (one 5' to 3', the other 3' to 5').
   • The strands twist around each other to form a right-handed double helix. This helical structure produces:
     • Minor Groove: The narrower groove
     • Major Groove: The wider groove, which is crucial for protein-DNA interactions

Helical Forms of DNA:

• B-DNA: The most common form under physiological conditions. It has 10 base pairs (bp) per turn and a pitch of 3.6 nm.
• A-DNA: Right-handed helix with 11 base pairs per turn, forms under dehydrating conditions.
• Z-DNA: A left-handed helix with 12 base pairs per turn, usually found in regions with alternating purines and pyrimidines.

3. Base Pairing:
   • DNA: Adenine (A) pairs with Thymine (T), and Guanine (G) pairs with Cytosine (C).
   • RNA: Adenine (A) pairs with Uracil (U), and Guanine (G) pairs with Cytosine (C). In some cases, G-U base pairs are formed in RNA.

Representation of DNA Sequences:

• DNA sequences are typically written in the 5' to 3' direction, reflecting the direction of synthesis.
• When describing sequences of neighboring bases (e.g., dinucleotides), it’s common to use the notation CpG to indicate a cytosine covalently linked to a neighboring guanosine via a phosphodiester bond.

Hairpin Structures in RNA:

• Hairpins are secondary structures commonly formed in RNA where a single strand folds back on itself, creating a stem-loop structure.
  • Stem: Double-stranded region formed by complementary base pairing.
  • Loop: The unpaired section of the strand, often involved in biological functions.
  • Hairpins play roles in gene regulation, mRNA stability, and serve as recognition sites for proteins.

DNA Replication:

Overview:

DNA replication is a semi-conservative process in which each new double helix consists of one original strand and one newly synthesized strand. Replication begins at specific sites called origins of replication and involves multiple enzymes.

Key Enzymes and Proteins in DNA Replication:

1. Helicase:

   • Unwinds the double-stranded DNA, creating the replication fork.

2. Single-Strand Binding Proteins (SSBs):

   • Stabilize the unwound DNA strands and prevent them from re-annealing.

3. Topoisomerase:

   • Relieves the tension caused by unwinding the DNA by cutting and rejoining the strands.

4. Primase:

   • Synthesizes a short RNA primer that provides a free 3'-OH group for DNA polymerase to begin synthesis.

5. DNA Polymerase:

   • Adds nucleotides to the growing DNA strand in the 5' to 3' direction, using the original strand as a template. It also has proofreading abilities to ensure fidelity.

6. DNA Ligase:

   • Joins Okazaki fragments on the lagging strand by forming phosphodiester bonds between nucleotides.

Leading vs. Lagging Strand:

• Leading Strand:
  • Synthesized continuously in the 5' to 3' direction towards the replication fork.
• Lagging Strand:
  • Synthesized discontinuously as short fragments (Okazaki fragments) in the 5' to 3' direction, but away from the replication fork. The fragments are later joined by DNA ligase.

Replication Fork and Directionality:

The replication fork progresses in both directions from the origin of replication, with the leading strand synthesized continuously and the lagging strand synthesized in fragments.

DNA Polymerase Function in Detail

• DNA Polymerase:
  • Main Role: Synthesizes new DNA by adding nucleotides to the 3’ end of a primer.
  • Proofreading: DNA polymerases have 3’ to 5’ exonuclease activity, allowing them to remove incorrectly paired bases and ensure high fidelity during replication.

Types of DNA Polymerases:

1. Prokaryotic:
   • DNA Polymerase I: Replaces RNA primers with DNA, has both exonuclease and proofreading activity.
   • DNA Polymerase III: Main enzyme for DNA replication, synthesizes the bulk of DNA.
2. Eukaryotic:
   • DNA Polymerase α: Initiates synthesis by creating RNA-DNA primers.
   • DNA Polymerase δ: Synthesizes the lagging strand and plays a major role in proofreading.
   • DNA Polymerase ε: Synthesizes the leading strand.

Transcription Overview:

Transcription is the process by which an RNA molecule is synthesized from a DNA template. This process involves:

1. RNA Polymerase: The enzyme that catalyzes RNA synthesis.
2. Template Strand: The strand of DNA used as a template for RNA synthesis.
3. Promoter: A specific DNA sequence where RNA polymerase binds to initiate transcription.
4. Sense Strand: The non-template strand of DNA, which has the same sequence as the RNA (except U for T).

RNA Polymerase:

• RNA Polymerase I: Transcribes rRNA.
• RNA Polymerase II: Transcribes mRNA.
• RNA Polymerase III: Transcribes tRNA and other small RNAs.

Gene Expression:

• Genes are transcribed into RNA, which is then translated into polypeptides.
• Transcription Factors: Proteins that bind to specific promoter regions on DNA to guide RNA polymerase.
• Promoter Elements:
  • TATA Box: Located ~25 bp upstream of the transcription start site, important for initiating transcription.
  • GC Box: Often found in housekeeping genes, it regulates the efficiency of transcription initiation.
  • CAAT Box: Located further upstream (~80 bp) and enhances promoter activity.

Key Terminologies:

• Antiparallel: The opposite orientation of the two strands of DNA, with one running 5' to 3' and the other 3' to 5'.
• Phosphodiester Bond: A chemical bond that joins the 3' carbon of one sugar to the 5' carbon of the next sugar.
• Okazaki Fragments: Short DNA fragments synthesized on the lagging strand during DNA replication.
• Promoter: A DNA sequence that binds RNA polymerase and initiates transcription.
• Hairpin: A secondary structure in RNA where the strand folds back on itself, forming a loop.

This set of notes covers nucleic acid structure, DNA replication, transcription, and essential enzymatic functions. If you'd like a visual aid or further clarifications, let me know!