L3 - DNA & Translation

Lecture Outline and Key Concepts

Lecture Overview

  • Content Coverage: Pierce Ch 10, Ch 13.1-2, 4, Ch 14, Ch 16.1

  • Learning Objectives: At the end of today’s lecture, students should be able to:

    1. Explain the functional significance of packaging DNA into chromosomes and discuss the lack of correlation between chromosome size and genetic information content.

    2. Describe structural differences between RNA and DNA and how these differences influence their respective functions.

    3. Identify the different types of RNA present in our cells and their specific functions.

    4. Explain how eukaryotic RNA polymerases are directed to begin and end transcription at specific sites, along with the process of transcription itself.

    5. Describe eukaryotic mRNA processing after transcription and mechanisms of mRNA decay.

DNA Packaging

  • Chromosomal Structure Understanding:

    • Chromosomal arms contain actively transcribed regions.

    • DNA packing can vary over time and in different genomic regions.

Types of Chromatin

  • Heterochromatin:

    • Always tightly packed, found at centromeres and telomeres.

  • Euchromatin:

    • Loosely packed, packing varies throughout the cell cycle.

Specific Chromosomal Structures

  • Centromeres:

    • Do not have specific sequences; resemble other chromosome parts due to epigenetic changes, crucial for kinetochore and spindle microtubule binding during cell division.

  • Telomeres:

    • Composed of repeated AT sequences, often followed by G.

    • Not replicated, leading to gradual shortening over time in somatic cells, with proteins binding that create a stabilizing 'cap'.

  • Consideration: What failures occur when chromosomes lose their centromeres during cell division?

Characteristics of Chromatin

Characteristic

Euchromatin

Heterochromatin

Chromatin Condensation

Less condensed

More condensed

Location

On chromosome arms

At centromeres, telomeres, and specific regions

Type of Sequences

Unique sequences

Repeated sequences

Presence of Genes

Many genes

Few genes

Timing of Replication

Throughout S phase

Late S phase

Transcription

Often

Infrequent

Crossing Over

Common

Uncommon (only for constitutive heterochromatin)

Types of DNA Sequences in Eukaryotic Chromosomes

  • Unique-sequence DNA:

    • Includes most protein-coding genes.

    • Can include similar protein-coding genes within gene families due to gene duplications (e.g., globin genes).

  • Repetitive DNA: (comprises ~50% of the genome)

    • Moderately Repetitive:

    • Length: 150-300 base pairs (bp)

    • E.g., rRNA genes, tRNA genes.

    • Includes unknown DNA segments and both tandem and interspersed repeat sequences (often transposable elements).

    • Highly Repetitive DNA: (or satellite DNA)

    • Short (< 10 bp), clustered,

    • Found in telomeres and centromeres.

    • Functions are largely unknown.

Human Genome Insights

  • Estimate of the Number of Protein-Coding Genes:

    • Initial estimate: 30,000 - 40,000; Current estimate (2023): 20,000 - 25,000 genes based on first human genome project completed around 2004.

  • Comparison to Other Organisms:

    • Organisms range:

    • Fruit fly: 13,600 genes

    • C. Elegans: 20,000 - 25,000 genes

    • Rice: 45,000 genes

    • Maize: 50,000 genes

Think About: Gene Expression

  • Every cell in the human body contains the same genomic information, but cells can exhibit significant differences due to differential gene expression.

Structures of RNA

  • General RNA Structure:

    • RNA is composed of nucleotides, featuring:

    • Sugar (Ribose in RNA), with a hydroxyl (–OH) group on the 2’ carbon (not present in DNA).

    • Phosphate group.

    • Nitrogenous bases (A, G, C, U in RNA vs A, G, C, T in DNA).

    • RNA molecules are typically single-stranded but can form complex secondary structures.

Comparison Between RNA and DNA

Characteristic

DNA

RNA

Type of Sugar

Deoxyribose

Ribose

Presence of 2’-OH Group

No

Yes

Bases

A, G, C, T

A, G, C, U

Strands

Usually double

Usually single

Stability

Stable

Easily degraded

RNA as Genetic Material

  • Historical Context: Evidence suggests RNA originated as the original genetic material (as self-replicating ribozymes) approximately 3.5 - 4 billion years ago.

Types of RNA in Eukaryotic Cells

  • Classes of RNA:

    • mRNA (Messenger RNA): Carries genetic code for proteins.

    • rRNA (Ribosomal RNA): Structural and functional component of ribosomes.

    • tRNA (Transfer RNA): Functions in translation by transferring amino acids to the growing polypeptide chain.

    • ncRNA (Non-coding RNA): A variety of classes and roles.

    • Examples include: snRNA, snoRNA, miRNA, siRNA, piRNA, crRNA, lncRNA.

Transcription Process

  • Definition: Synthesis of RNA from a DNA template.

  • Key Needs for Transcription:

    1. DNA template for the transcription unit (only one strand transcribed).

    2. Raw materials (e.g., ribonucleotide triphosphates).

    3. Transcription apparatus consisting of proteins necessary for synthesizing RNA, including RNA polymerase.

  • Transcription Characteristics:

    • Occurs when DNA is accessible (euchromatin).

    • Each gene is transcribed from one of the two DNA strands (template strand).

    • Important regulatory step for gene expression management.

Anatomy of a Protein Coding Gene

  • Consists of a promoter, RNA-coding region, and terminator sequence:

    • Promoter: Not transcribed; indicates transcription start.

    • Terminator: Sequence indicating transcription stop (normally transcribed, part of RNA).

    • RNA Coding Sequence: Comprised of exons and introns (exons are expressed; introns are removed during mRNA maturation).

Transcription Mechanics

  • Transcription yields an antiparallel complementary RNA sequence compared to the DNA template.

  • Unlike DNA replication, transcription does not require a primer, and DNA only unwinds in the transcription bubble, allowing synthesis.

Example of Transcription Analysis

  • If the nontemplate strand is 5’ -ATG TTT GAA TGG- 3’, the corresponding mRNA sequence post-transcription would involve determining the correct base pairing and sequence from the provided DNA templates.

  • Note: Review practice problems discussed in class to reinforce understanding further.

Ensure understanding and recognition of differential expression of genes across cell types and during various conditions.