Lecture_2_Notes for Biochem

Principles of Cellular Function & Biochemistry I

• Dr. Manos C. Vlasiou, MRSC, PhD, CChem

Nucleic Acids

Structure of Nucleic Acids

• Monomeric units: Nucleotides.

• Sugar backbone:

  • Ribose: RNA

  • Deoxyribose: DNA

• Phosphate backbone.

• Base pairs: Hydrogen bonds between nitrogenous bases.

  • Adenine (A) pairs with Thymine (T) in DNA, and Uracil (U) in RNA.

  • Guanine (G) pairs with Cytosine (C).

• Structure types:

  • DNA: Double stranded (double helix)

  • RNA: Single stranded

Learning Objectives

1. Describe the basic structure of nucleic acids and compare the structures of DNA and RNA.

2. Discuss hydrogen bonding and its importance in the structure of the double DNA helix.

3. Describe hierarchical organization within the nucleus, including histones, chromatin, and chromosomes.

4. Describe DNA replication in prokaryotic and eukaryotic organisms.

Nucleotides

Key Concepts

• Nitrogenous bases of nucleotides:

  • Purines: Adenine (A), Guanine (G)

  • Pyrimidines: Cytosine (C), Uracil (U), Thymine (T)

• Structure of a nucleotide:

  • Nitrogenous base + Ribose/deoxyribose + one or more phosphate groups.

• DNA contains adenine, guanine, cytosine, and thymine.

• RNA contains adenine, guanine, cytosine, and uracil.

Nucleotide Functionality

• Eight varieties of nucleotides exist: each has a nitrogenous base linked to a sugar with at least one phosphate group.

• Purines: Adenine (A), Guanine (G).

• Pyrimidines: Cytosine (C), Uracil (U), Thymine (T).

• Ribonucleotides: Contain ribose.

• Deoxyribonucleotides: Contain deoxyribose.

ATP: Energy Carrier

• Best known nucleotide: Adenosine triphosphate (ATP), used for cellular work:

  • Biosynthetic reactions

  • Ion transport

  • Cell movement

Nucleic Acid Structure

Key Concepts

• Phosphodiester bonds link nucleotides in DNA and RNA.

• DNA double helix: two antiparallel strands.

• RNA: usually single-stranded, may form intramolecular pairs.

Watson-Crick Model of DNA

Major Features

1. Two polynucleotide chains form a double helix.

2. Strands are antiparallel (run in opposite directions).

3. Bases occupy the core; sugar-phosphate chains at the periphery, minimizing repulsion.

4. Contains major and minor grooves.

Single-stranded vs. Double-stranded Structure

• Single-stranded DNA: Rare, primarily in viruses.

• RNA: Single strands forming compact structures; catalyze reactions and bind small organic molecules.

DNA Carries Genetic Information

• DNA's double-stranded nature facilitates replication.

• Each strand acts as a template for complementary strand synthesis.

Histones & Chromatin

Key Points

• Histones are proteins that compact chromosomal DNA.

• Forms a DNA-protein complex known as chromatin.

• Histones induce folds and compress DNA to fit in the nucleus.

• DNA is negatively charged; histones are positively charged, allowing tight binding.

Chromatin Structure

• Chromatin: Template of DNA structure:

  • 2 nm DNA double helix

  • "Beads on a string" form 11 nm

  • 30 nm chromatin fiber

Chromosomes

• Composed of DNA tightly wound around histones.

• Nucleosomes: DNA wraps around histone proteins.

Central Dogma of Molecular Biology

• Flow of genetic information:

  • DNA replication

  • Transcription: DNA to RNA

  • Translation: RNA to protein

Transcription & Translation

Overview

1. DNA directs synthesis of mRNA.

2. mRNA is translated by tRNA at the ribosome, adding specific amino acids to form proteins.

Nucleic Acid Sequencing

Techniques

• Restriction enzymes cleave specific DNA sequences.

• Electrophoresis separates DNA fragments by size.

• Chain-termination method defines DNA sequences.

Mutations

Introduction

• Mutations can arise from DNA replication errors or damage from external factors (chemicals/radiation).

• Types include: Insertion, Deletion, Substitution.

Manipulating DNA

• Cloning: Producing identical DNA segments.

• DNA libraries: Collections of cloned DNA segments.

• PCR: Amplifies DNA segments by synthesizing complementary strands.

Practical Applications of Recombinant DNA Technology

• Cloned genes can be expressed in host organisms.

• Site-directed mutagenesis allows for selective changes in nucleotide sequences.

Summary of Key Concepts

1. Nucleotides: Components of nucleic acids.

2. Structure: DNA double helix and RNA's diverse shapes.

3. Function: DNA as a genetic repository, transcription, and translation mechanisms.

4. Sequencing: Cutting and measuring DNA fragments.

DNA Structure Variability

Different Forms

• DNA can adopt A, B, or Z conformations.

• Supercoiling: Affects DNA's compactness.

• Topoisomerases regulate supercoiling levels.

Supercoiling & Topoisomerases

• Type I: Single-strand break; relaxes supercoils.

• Type II: Double-strand break; alters supercoiling levels.

Structural Stability of Nucleic Acids

Stabilization Mechanisms

• Base pairing, stacking interactions, ionic interactions stabilize nucleic acids.

• Hydrogen bonds contribute relatively weakly to structural stability.

Denaturation & Renaturation

• DNA denaturation: Separation of strands at high temperature, described by hyperchromic effect.

• Renaturation can occur upon cooling.

RNA Structures

• RNA can adopt numerous structural configurations, including double-stranded segments.

Antitumor Antibiotics & DNA Structures

• Interaction of antibiotics with DNA: Promotes specific structures that contribute to cytotoxic effects.