From DNA to Protein: Gene Expression and Transcription in Eukaryotic Cells

Ch.7. From DNA to Protein: How Cells Read the Genome

Introduction to Gene Expression

The flow of genetic information in living cells is from DNA to RNA and then to protein. This process, known as the Central Dogma of molecular biology, is fundamental to cell function and identity. This chapter discusses the basic principles of gene expression from the perspective of cell biology.

• Gene Expression: The process by which genetic information encoded in DNA is translated into functional products, such as proteins.

• Transcription: The synthesis of RNA from a DNA template.

• Translation: The synthesis of proteins from an RNA template.

Diversity and Unity of Cells

All somatic cells in an organism have the same DNA, but gene expression at specific sets of genes in a cell determines its unique structure and function.

• Neurons, Lymphocytes, and Cardiomyocytes all share the same genome but differ in structure and function due to differential gene expression.

Central Dogma: From DNA to Protein

Overview

Genes provide instructions for making proteins, but not all genes are transcribed at the same rate or at the same time. Cells only make a protein when it is needed.

• Transcription and Translation are the two main processes that transfer genetic information from DNA to protein.

• RNA acts as an intermediate molecule in protein synthesis.

Gene Expression in Eukaryotic Cells

Gene expression is a complex process regulated at multiple levels and by many factors.

• Most somatic cells have the same DNA, but gene expression determines cell type and function.

• Not all DNA sequences are transcribed into RNA.

Transcription: From DNA to RNA

RNA Structure and Function

There are three major types of RNA: mRNA, tRNA, and rRNA. RNA differs from DNA in two key ways:

• The sugar in RNA nucleotides is ribose (not deoxyribose).

• The base uracil (U) in RNA replaces thymine (T) found in DNA.

• RNA is single-stranded and can fold into different shapes.

RNA Structure Example

RNA molecules can form complex three-dimensional shapes due to their single-stranded nature and base pairing, which is important for their function.

Types of RNA Produced in Cells

Table: Types of RNA and Their Functions

Type of RNA	Function
mRNA	Codes for proteins
rRNA	Forms the core of the ribosome and catalyzes protein synthesis
tRNA	Serves as adaptors between mRNA and amino acids during protein synthesis
Other small RNAs	Regulate gene expression, RNA splicing, telomere maintenance, and many other processes

Transcription Machinery

Key Components

• Template: One strand of the DNA double helix is used as a template to determine the nucleotide sequence of RNA.

• Monomers: Nucleotides (ATP, GTP, UTP, CTP) are the building blocks for RNA synthesis.

• RNA Polymerase: The enzyme that catalyzes the polymerization reaction.

• Transcription Factors: DNA binding proteins that regulate the transcription process.

Transcription Process

• RNA polymerase binds to the DNA template and synthesizes RNA in the 5' to 3' direction.

• Transcription factors help regulate the speed, frequency, and initiation of transcription.

RNA Polymerases in Cells

Table: RNA Polymerases in Eukaryotic Cells

Type of Polymerase	Genes Transcribed
RNA Pol I	rRNA genes
RNA Pol II	Protein-coding genes, snRNA genes, some small RNAs
RNA Pol III	tRNA genes, 5S rRNA genes, other small RNAs

Comparison

• Bacteria and archaea have only one RNA polymerase.

• Eukaryotic cells have three different RNA polymerases, each responsible for transcribing different types of RNA.

Basic Structure of a Gene

Gene Organization

• Promoter: A regulatory region of DNA located upstream of the coding region; serves as the initiation point for gene transcription.

• Coding Region: The part of the gene that is transcribed into RNA.

• Terminator: The region where transcription ends.

Template and Coding Strands

• Template Strand: The DNA strand used by RNA polymerase to attach complementary bases during transcription.

• Coding Strand: The DNA strand whose sequence matches the RNA transcript (except T is replaced by U).

Transcription Initiation and Promoters

Promoter Elements

• Promoters contain specific DNA sequences, such as the TATA box, which are recognized by transcription factors.

• TATA-binding protein (TBP) is a transcription factor that binds to the TATA box and helps initiate transcription.

Transcription Process in Bacteria

• Assembly: RNA polymerase recognizes the promoter region.

• Initiation: RNA polymerase starts using one of the DNA strands as a template.

• Elongation: RNA polymerase advances along the template, synthesizing RNA.

• Termination: RNA polymerase reaches the terminator and ends transcription.

• Sigma factor: A subunit of RNA polymerase that specifically binds to the promoter and initiates transcription in bacteria.

Transcription in Eukaryotes

• Requires many transcription factors (e.g., TBP, TFIID, TFIIH).

• Promoters often contain a TATA box sequence.

mRNA Processing

Processing Steps

• 5' capping: Addition of a methylated guanine (G) at the 5' end.

• 3' poly(A) tail: Addition of a stretch of 100-200 adenosines (A) at the 3' end.

• Splicing: Removal of introns and joining of exons.

Differences Between Prokaryotes and Eukaryotes

• In prokaryotes, transcription and translation can occur simultaneously.

• In eukaryotes, primary RNA transcripts undergo processing to produce functional mRNA.

Key Equations and Rules

Base Pairing Rule

• During transcription, RNA nucleotides pair with complementary DNA bases:

$A_{DNA} \rightarrow U_{RNA}$ $T_{DNA} \rightarrow A_{RNA}$ $C_{DNA} \rightarrow G_{RNA}$ $G_{DNA} \rightarrow C_{RNA}$

Direction of RNA Synthesis

• RNA is synthesized in the 5' to 3' direction:

$\text{RNA polymerase always moves in the 5' \rightarrow 3' direction}$

Summary

• Gene expression is the process by which genetic information is converted into functional products.

• Transcription and translation are the key steps in gene expression.

• RNA polymerases and transcription factors are essential for transcription.

• mRNA processing is required in eukaryotes before translation can occur.

Additional info: Some details about transcription factors and mRNA processing were expanded for clarity and completeness.