Gene Expression at the Molecular Level I

: Production of mRNA and Proteins

What is Gene Expression?

The process of turning a gene’s information into a functional product (like a protein).

What levels are gene expression studied at?

• Molecular level (DNA → RNA → protein)

• Trait level (how the protein affects appearance or function)

What is a Mutation?

Heritable change in genetic material (DNA).

What is the effect of a Mutation?

Can alter the gene sequence → may change how the gene works.

Why Mutations Matter in Biology Research

Helped show:

• Normal genes → functional proteins

• Mutated genes → altered or non-functional proteins

Example of gene mutation

Red hair is caused by a mutation in the MC1R gene, leading to a protein that functions differently.

This shows how a gene change can directly affect a visible trait.

What did Archibald Gerrod study?

Patients with metabolic defects (e.g., alkaptonuria)

What is Alkaptonuria?

An inherited disease where the body accumulates high levels of homogentisic acid (alkapton).

Cause of alkaptonuria

A defect in the enzyme that normally breaks this substance down.

What did Garrod Propose in1908

a connection between:

• Inheritance of a mutant gene

• A missing or defective enzyme

• A resulting metabolic disease

Inborn Error of Metabolism

Garrod’s term for diseases caused by defects in genetic material that lead to faulty or missing enzymes.

Core idea of inborn metabolism

Gene mutation → enzyme defect → metabolic disorder

Gene mutation → enzyme defect → metabolic disorder

Phenylalanine: An amino acid your body must break down.
Normal process: Phenylalanine → Tyrosine (using an enzyme)

What is Penylalanine hydroxylase (PAH) and its function?

Enzyme: Phenylalanine hydroxylase (PAH)
Function: Converts phenylalanine into tyrosine.

What Happens if the Penylalanine hydroxylase enzyme Is Defective?

Phenylalanine cannot be properly broken down. This leads to a build-up of phenylalanine in the body.

Why Is the Build-Up Penylalanine hydroxylase Dangerous?

High phenylalanine levels can damage the developing brain → Phenylketonuria (PKU).

What does a mutation in a gene typically lead to in metabolic pathways?

Answer: A defective enzyme → metabolic build-up → metabolic disease.

What did Beadle and Tatum rediscover in the early 1940s?

The work of Archibald Garrod on the relationship between genes, enzymes, and metabolic defects.

What organism did Beadle and Tatum study, and why?

Neurospora crassa (bread mold) because it can make all cellular components from just sugar, inorganic salts, and biotin.

What was Beadle & Tatum’s main hypothesis?

That genes encode enzymes, and amino acid synthesis occurs through a pathway where each gene controls a different enzyme.

How can gene mutations affect Neurospora’s growth?

Mutations can cause missing enzymes, preventing the mold from making certain amino acids.

What did the mutated Neurospora strains require to grow?

Media supplemented with arginine, meaning they couldn’t synthesize it themselves.

Why did researchers expect at least three genes in the arginine pathway?

Because the synthesis likely involved three precursor molecules, meaning three steps and three enzymes.

How did Beadle & Tatum test the mutant strains?

By providing different precursor molecules (ornithine, citrulline, arginine) to see which ones allowed growth.

What determined whether a mutant strain could grow with certain precursors?

Which specific gene (and therefore which enzyme) was defective.

What major conclusion did Beadle and Tatum reach?

One gene controls the synthesis of one enzyme — the one gene–one enzyme hypothesis.

Which precursors allow growth for each mutant type?

• Some grow with ornithine, citrulline, arginine

• Others grow with citrulline and arginine only

• Final group grows with arginine only

Why is the one gene–one enzyme hypothesis incomplete?

• Because enzymes are only one type of protein.

How do multi-subunit proteins challenge the one gene–one enzyme idea?

Some proteins (e.g., hemoglobin) have multiple polypeptides, each encoded by a different gene.

How does alternative splicing show that the hypothesis is oversimplified?

A single gene can be spliced in different ways to produce multiple polypeptides.

Why do non-coding genes challenge the original hypothesis?

Some genes produce RNAs that do not make proteins, showing genes don’t always encode enzymes or polypeptides.

What is the Central Dogma of Molecular Biology?

The flow of genetic information in cells: DNA → RNA → Protein.

What is DNA replication?

The process by which DNA makes an identical copy of itself before cell division.

What are the building blocks of DNA?

Nucleotides, each consisting of a sugar, phosphate, and nitrogenous base

What is transcription?

RNA synthesis from a DNA template. Produces an RNA strand complementary to DNA.

What does RNA do in gene expression?

Acts as the messenger (mRNA) carrying genetic information from DNA to ribosomes.

What are amino acids?

The building blocks of proteins.

What determines a protein’s function?

The sequence and structure of its amino acids.

Do prokaryotes have a membrane bound nucleus?

No

What is the major difference in gene expression between prokaryotes and eukaryotes?

• Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm.

• Eukaryotes: Transcription occurs in the nucleus, translation in the cytosol, with RNA processing in between.

Where does transcription occur in prokaryotes?

In the cytoplasm, directly from the DNA.

When and where does translation occur in prokaryotes?

Immediately after transcription, in the cytoplasm, often while mRNA is still being synthesized.

Why can transcription and translation occur simultaneously in prokaryotes?

Because prokaryotes lack a nucleus, so ribosomes can access mRNA as soon as it forms.

Where does transcription occur in eukaryotes?

In the nucleus, producing pre-mRNA.

What happens during RNA processing in eukaryotes?

Pre-mRNA is modified (capping, splicing, poly-A tail) to become mature mRNA.

How does mRNA leave the nucleus in eukaryotes?

Through a nuclear pore, entering the cytosol for translation.

Where does translation occur in eukaryotes?

In the cytosol, at ribosomes.

One-sentence comparison of prokaryotic vs. eukaryotic gene expression?

• Prokaryotes: Transcription → Translation (no processing, same place, same time).

• Eukaryotes: Transcription → RNA processing → Translation (different places, sequential).

What is a gene?

A gene is an organized unit of DNA that is transcribed into RNA and produces a functional product.

What do protein-coding genes produce?

They are transcribed to make mRNA, which specifies the amino acid sequence of a polypeptide.

What is the functional product of a protein-coding gene?

The polypeptide (the protein), not the mRNA.

Why is mRNA considered an intermediary?

Because mRNA carries the genetic message from DNA to the ribosome for translation into a polypeptide.

What is the final functional product of non-coding RNA genes?

The RNA itself — they are not translated.

What are examples of non-coding RNAs?

tRNA and rRNA.

What is a promoter?

A DNA sequence where RNA polymerase binds to start transcription.

What is a terminator?

A sequence that signals RNA polymerase to stop transcription.

What is the transcribed region?

The part of the gene that is copied into RNA.

What is a regulatory sequence?

A DNA segment that helps control when, where, and how much a gene is expressed.

What happens in initiation?

Sigma factor guides RNA polymerase to the promoter, DNA unwinds, forming an open complex.

How is RNA synthesized?

RNA grows 5' → 3' using the template strand; U replaces T.

Template vs coding strand?

Template strand = copied by RNA.
Coding strand = same as mRNA (T → U).

How is RNA polymerase different from DNA polymerase?

No primer needed, no proofreading, no exonuclease.

What happens in termination?

RNA polymerase reaches terminator → RNA and DNA released.

Can the DNA template strand change between adjacent genes?

Yes, it can vary depending on the promoter.

What direction is RNA synthesized?

5’ → 3’.

What direction is the template DNA strand read?

3’ → 5’.

Is one DNA strand always the template strand for all genes?

No, each gene can use a different strand.

What direction are genes A & B transcribed?

Left → right.

What direction is gene C transcribed?

Right → left.

Can gene C overlap with gene B? Why?

Yes, because they use different template strands, so sequences differ.

Are the basic features of transcription the same in prokaryotes and eukaryotes?

Yes, bur eukaryotes use more complex protein components

How many RNA polymerases do eukaryotes have?

Three (i, ii, iii)

How many RNA polymerases do prokaryotes have?

One

What replaces the sigma factor in eukaryotes?

Five general transcription factors.

What does phosphorylation of RNA polymerase do?

Helps it release the promoter and begin elongation.

Why is phosphorylation important?

It allows different genes in the genome to be transcribed.

What is the promoter region?

A DNA sequence where RNA polymerase binds to start transcription.

Why does eukaryotic RNA need processing?

The first RNA made (pre-mRNA) is not ready and must be processed.

What is splicing?

Removing introns and joining exons (exons stay)

Do introns or exons get removed?

Introns

Does the mRNA stay in the nucleus after processing?

No, it exits the nucleus.

What does RNA processing remove?

Gene regions that don’t code—introns.

What modifications are added to pre-mRNA?

5' cap and 3' poly-A tail.

What is the product after splicing + capping + tailing?

What is the order of splicing, capping, tailing, transcription?

Transcription, capping, tailing, splicing

What is capping?

Adding 7-methylguanosine to the 5’ end of the mRNA (5’ cap).

When does capping occur?

While RNA polymerase is still making the pre-mRNA.

What recognizes the 5’ cap?

Cap-binding proteins.

Why is the 5’ cap important?

Needed for mRNA to exit the nucleus, protects mRNA, and helps ribosome binding.

What helps translation start?

The 5’ cap (binds to the ribosome).

What is the first base at the 5’ end?

A sugar-phosphate.

How is the 5’ cap attached?

A guanine linked to 3 phosphates.

At what transcript length does capping happen?

When the RNA is ~20–25 nucleotides long.

What is tailing?

Adding 100–200 adenines to the 3’ end (poly-A tail).

What triggers tailing?

A poly-adenylation sequence that attracts an enzyme complex

What does the poly-A tail help with?

Export from the nucleus and increased mRNA stability.

Why is mRNA stability important?

Lasts longer and makes more protein.

What happens if the poly-A tail is long?

More stable → lasts longer → more protein.

What happens if the poly-A tail is short?

Less stable → degraded sooner → less protein.

Can cells change tail length?

Yes, cells can adjust how long the tail is.