Chapter 4: DNA & Gene Expression

What is DNA?

The molecular script of life. Every living cell carries its won copy of this script, written in a four-letter chemical code that determines traits, diseases, and inheritance. Understanding its structure allows biotechnology to read, copy, and edit the language of heredity.

What is DNA made up of?

Two long chains of nucleotides that wind around each other to form a double helix. Each nucleotide has three parts: a phosphate group, a deoxyribose sugar, and a nitrogenous base.

What shape is DNA?

The helix shape ensures stable storage of genetic information and faithful replication.

What is each nucleotide made up of?

Each has three parts: a phosphate group, a deoxyribose sugar, and a nitrogenous base.

What is the backbone of DNA?

The sugar and phosphate form the backbone.

How are the rungs of the ladder connected together?

The hydrogen bonds connect the two strands.

What are the four nitrogen bases?

Adenine, Thymine, Cytosine, Guanine.

How do the nitrogenous bases of DNA pair?

Bases pair by hydrogen bonding. Adenine always pairs with Thymine (two hydrogen bonds) and Cytosine always pairs with Guanine (three hydrogen bonds).

What do the sequence of bases code?

It encodes the instructions for building proteins.

How does Biotechnology use DNA’s stability and reproducibility?

Biotechnology uses DNA for PCRs, Gene Sequencing, and Genetic Engineering.

What does understanding the structure of DNA allow?

Knowing how DNA’s structure dictates its functions is the foundation for modern biotechnology and genetic medicine.

When does DNA replication occur?

Occurs in the S phase of the cell cycle.

What is semiconservative replication?

Each new molecule contains one old strand and one new strand.

How does the DNA double helix unwind?

Enzymes separate the strands.

What is the replication fork?

Marks the region where the DNA is opening.

What is the leading strand?

The complementary strand that is built continuously.

What is the lagging strand?

The strand of DNA that is built in fragments.

What type of DNA does bacteria have?

Bacteria has a singular, circular chromosome.

What is DNA polymerase?

A type of enzyme that attaches at the origin of replication to separate the DNA strands and building new complimentary strands.

What is the Origin Recognition Complex?

Detects and binds to the Origin of Replication (specific DNA sequence). It also marks where replication begins.

What is Helicase?

Unwinds the DNA double helix by breaking hydrogen bonds between base pairs.

What is the purpose of the template DNA?

Original DNA strands that serve as guides to build complementary new strands.

What is the Replication bubble?

Formed where DNA strands separate and expands as replication proceeds in both directions.

What is the replication fork?

The “Y” shaped region where DNA is actively unwound and copied.

What are topoisomerases?

Prevent DNA from unwinding ahead of the fork by making temperature cuts. Essential for relieving torsional stress during replication.

What are single-stranded binding proteins?

Bind to unpaired DNA strands to keep them from reattaching and stabilizes the open replication fork.

What are RNA primers?

Short RNA sequences synthesized to start DNA synthesis.

What is primase?

Enzyme that synthesizes RNA primers on both strands.

What are Okazaki fragments?

Short stretches of newly synthesized DNA joined later into a continuous strand.

What is DNA ligase?

Enzyme that joins Okazaki fragment and is the final step to ensuring a complete strand.

What are histones proteins?

Small, positively charged proteins that bind DNA, allowing it to coil tightly.

What are histones?

Proteins, where eight of them from a core around which DNA unwinds.

What are nucleosomes?

The basic unit of chromatin, consisting of DNA wrapped around histones.

What is chromatin?

The entire DNA-protein complex visible in the nucleus.

What are euchromatin?

Loosely packed and active chromatin.

What are heterochromatin?

Tightly packed and inactive chromatin.

Who discovered transformation?

Frederick Griffith.

When was transformation discovered?

1928

What is the end conclusion of DNA transformation?

Genetic information could be transferred between bacteria, specifically that heritable information could be passed between organisms without direct reproduction.

What is transcription?

The process where the genetic information from a segment of DNA is copied into a new molecule of messenger RNA.

What is mRNA?

A single stranded RNA copy of DNA that carries genetic information to ribosomes. Formed through transcription, DNA acts as a template for mRNA synthesis.

What is a ribose phosphate backbone?

RNA’s sugar-phosphate structure that contains ribose instead of deoxyribose.

What is a codon?

A sequence of three RNA bases that code for a specific amino acid.

What is a polypeptide?

A chain of amino acids linked by peptide bonds and fold into function proteins.

What is an enzyme?

A biological catalyst formed from the polypeptide that speeds up specific chemical reactions.

What is the central dogma of molecular biology?

The process of DNA to mRNA to Protein to Trait in molecular biology.

Why is it important to understand the structure of RNA in biotechnology?

RNA molecules are critical intermediaries between our genetic code (DNA) and the proteins that perform nearly every cell function.

How are RNA used to treat disease and create new therapies?

Scientists now use mRNA vaccines (like COVID-19 vaccines), gene therapy, and CRISPR technology to manipulate RNA.

What makes RNA unstable?

RNA contains ribose, a 5-carbon sugar with an extra oxygen atom compared to DNA’s deoxyribose, making RNA more chemically reactive.

What is the ribose-phosphate backbone?

Phosphate groups link to ribose sugars to form the RNA backbone.

What makes DNA more stable?

DNA’s backbone lacks one oxygen atom on each sugar.

When does uracil pair with thymine?

Protein synthesis.

What are the three key differences between RNA and DNA?

RNA contains ribose (not deoxyribose), uses uracil (not thymine), and is typically single-stranded (not doubled-stranded).

What is messenger RNA?

A type of RNA in gene expression that carriers genetic instructions from DNA to ribosomes.

What is a codon?

A three-base sequence (triplet) on mRNA coding for one specific amino acid.

What are amino acids?

The building blocks of proteins.

What is an anticodon?

A three-base sequence on tRNA complementary to an mRNA codon. Ensures the correct amino acid is added during translation.

What do tRNA molecules do?

Act as adapters that “read” genetic code on mRNA and deliver the correct amino acids in proper sequence.

What does the cloverleaf shape of tRNA allow?

Allows the binding to both specific amino acids and complementary codons on mRNA.

What is the small ribosomal subunit?

The smaller component of a ribosome. Helps position mRNA and tRNA correctly during protein synthesis.

What is the large ribosomal subunit?

Contains the catalytic site for forming peptide bonds. Connects amino acids together to build protein chains.

What do ribosomes do?

The cell’s “protein factories” where mRNA, tRNA, and amino acids come together. They read mRNA codons, matches them with tRNA anticodons, and links amino acids into polypeptide chains that fold into functional proteins.

Why is it important to understand transcription?

Defects in these processes cause genetic diseases. Scientists now use antisense oligonucleotides and gene therapy to correct splicing errors, and mRNA vaccines technology depends on designing synthetic mRNA that cells can translate into therapeutic proteins.

What is RNA polymerase?

The essential enzyme that catalyzes transcription. Unwinds the DNA double helix and reads the template strand in the 3’ to 5’ direction. Synthesizes RNA in the 5’ to 3’ direction by adding complementary ribonucleotides.

What is pre-mRNA?

The initial RNA transcript produced directly from DNA in eukaryotic cells. Contains both coding sequences and non-coding sequences. Must be processed before leaving the nucleus.

What are exons?

The coding regions of pre-mRNA that will be kept. Contains the genetic instructions for amino acid sequences in proteins. Multiple exons are spliced together to form the final mRNA.

What are introns?

Non-coding regions that must be removed. Loop out during RNA processing and are cut away by the splice some. Does not code for proteins.

What is the 5’ cap?

A modified guanine nucleotide added to the beginning (5’ end) of mRNA. Protects mRNA from degradation by cellular enzymes. Required for ribosome binding and translation initiation.

What is a Poly-A tail?

A string of approximately 200 adenine nucleotides added to the 3’ end of mRNA. Protects the mRNA from degradation and increases mRNA stability. Helps with mRNA export from nucleus and enhances translation.

What percent of human genetic diseases is due to improper RNA splicing?

15%

What is the ribosomal complex?

Molecular machine that reads mRNA and assembles proteins. Made of rRNA and 50+ proteins. Has A, P, and E bindings sites for tRNA.

During translation, what happens at initiation?

Ribosome assembles on mRNA at start codon.

During translation, what happens at elongation?

RIbosome reads each codon (three bases). tRNA with complementary anticodon binds. Amino acid added to growing chain via peptide bonds. RIbosome move stop the next codon; empty tRNA exits.

During translation, what happens at termination?

At stop codon, completed polypeptide releases.

Why is gene regulation important?

It allows scientists to control when proteins are produced.

What is the regulator gene?

Encodes the repressor protein and is located away from the operon.

What is the promoter region?

DNA binding site for RNA Polymerase. Where transcription begins.

What is the operator region?

Control switch for gene expression. Repressor protein binds here to block transcription.

What is an inducer?

A molecule that initiates or increases gene expression.

What is the repressor protein?

Binds to the operator, blocking RNA polymerase. It also prevents transcription of structural genes.

What is the TRP operon?

Tryptophan molecules are corepressors that bind to inactive repressor proteins. Operon that acts as a corepressor, converting the inactive repressor into an active form that shuts down the operon.

What happens when tryptophan is absent?

The cell synthesizes all three enzymes necessary to produce this essential amino acid. This represents inducible gene expression—genes are turned on when their product is needed.

What happens when tryptophan is abundant?

It acts as a corepressor, converting the inactive repressor into an active form that shuts down the operon. This demonstrates negative feedback regulation—the end product inhibits its own synthesis, preventing wasteful enzyme production.

What is a point mutation?

Single base changes can have cascade effects throughout gene expression.

Why is it important to understand point mutations?

It is the foundation of genetic diseases. Understanding how a single base change cascades through transcription, translation, and protein function is essential for precision medicine, gene therapy design, and predicting disease severity from genetic testing results.

What is polymerase chain reaction?

The molecular “photocopier” that revolutionized medicine—enabling rapid COVID19 testing, cancer mutation screening, forensic DNA analysis, paternity testing, and detection of infectious diseases from tiny samples.

How did PCR revolutionize medicine?

Enabled rapid COVID19 testing, cancer mutation screening, forensic DNA analysis, paternity testing, and detection of infectious diseases from tiny samples.

What is the starting material for PCR?

Template DNA.

What are PCR tubes?

Thin-walled plastic tubes containing the reaction mixture.

What are primers?

Two short single-stranded DNA oligonucleotides (~15-30 bases long).

Where does the forward primer bind?

Binds to the 3’ end of one strand.

Where does the reverse primer bind?

Binds to the 5’ end of the complementary strand.

What are dNTPs?

The building blocks for new DNA synthesis. dATP, dCTP, dGTP, dTTP (the four DNA bases with attached sugars and phosphates).

What is Taq polymerase?

Enzyme that synthesizes new DNA strand. Originally isolated from Thermus aquaticus (bacteria living in hot springs).

Where is Taq polymerase isolated from?

Originally isolated from Thermus aquaticus (bacteria living in hot springs).

What does thermostable mean?

Survives repeated heating to 95 degrees Celsius without denaturing.

What are the three steps of PCR?

Initialization/Denaturation, Annealing, and Elongation.

What temperature does denaturation happen at?

95 degrees Celsius.

What happens during denaturation?

Sample is heated to approximately 95 degrees Celsius. The high temperature breaks hydrogen bonds between complementary base pairs. Results in double stranded DNA separating into two single strands. The separates template strands are now available for primer binding.

What temperature does annealing happen at?

55 degrees Celsius.