Chapter 4: DNA & Gene Expression- Calista Velasquez

What is DNA?

The molecular script of life.

What is DNA made up of?

Two chains of nucleotides that wind around each other to form a double-helix.

What shape is DNA?

Double-helix.

What is each nucleotide made up of?

A phosphate group, deoxyribose sugar, and nitrogenous base.

What is the backbone of DNA?

The sugar and phosphate.

How are the rungs of the ladder connected together?

The rungs are the nitrogenous bases connected through hydrogen bonds.

What are the four nitrogen bases?

Adenine, Thymine, Cytosine, Guanine.

How do the nitrogenous bases of DNA pair?

A+T, C+G

What do the sequence of bases code?

Instructions for building proteins.

How does biotechnology use DNA’s stability and reproducibility?

PCR, gene sequencing, and genetic engineering.

What does understanding the structure of DNA allow?

The foundation of modern biotechnology and genetic medicine.

When does DNA replication occur?

S phase.

What is semiconservative replication?

When in DNA replication, each new molecule contains one old strand and one new strand.

How does the DNA double helix unwind?

With the help of enzymes that separate the strands.

What is the replication fork?

Region where DNA is actively unwound and copied.

What is the leading strand?

Synthesized continuously, away from the fork. Requires one primer.

What is the lagging strand?

Synthesized discontinuously, away from the fork. Has Okazaki fragments.

What type of DNA does bacteria have?

Double-stranded circular DNA.

What is DNA polymerase?

Attaches to the Origin of Replication, building new complementary strands.

What is the Origin Replication Complex?

Detects and binds to the Origin of Replication, marks where replication begins.

What is Helicase?

Unwinds the DNA double-helix by breaking the hydrogen bonds.

What is the purpose of the template DNA?

Serves as guides to build complementary new strands.

What is the Replication bubble?

Formed where strands separate, expands as replication proceeds.

What is the replication fork?

Region where DNA is actively unwound and copied.

What are topoisomerases?

Prevents DNA from unwinding ahead of the fork by making cuts. Relieves stress during replication.

What are single-strand binding proteins?

Keeps unpaired DNA strands from reattaching by binding to them. Stabilizes the 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?

Stretches of newly synthesized DNA joined later into a continuous strand.

What is DNA ligase?

Enzyme that joins Okazaki fragments. It is the final step ensuring a complete strand.

What are histone proteins?

Eight histones form a core around which DNA unwinds.

What are histones?

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

What are nucleosomes?

Basic unit of chromatin, consists of DNA wrapped around histones.

What is chromatin?

The entire DNA-protein complex visible in the nucleus.

What are euchromatin?

Loosely-packed, active.

What are heterochromatin?

Tightly-packed, inactive.

Who discovered transformation?

Oswald Avery.

When was transformation discovered?

1944.

What was the end conclusion of DNA transformation?

Today it is used to insert genes into bacteria, making up basic genetic engineering and recombinant DNA technology.

What is transcription?

Makes DNA into mRNA.

What is mRNA?

A single-stranded copy of DNA that carries genetic information to ribosomes. Formed through transcription.

What is a ribose phosphate backbone?

RNA’s sugar-phosphate sturcture (ribose instead of deoxyribose)

What is a codon?

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

What is a polypeptide?

Chain of amino acids linked by peptide bonds. Becomes functional protein.

What is an enzyme?

A biological catalyst formed from polypeptide.

What is the central dogma of molecular biology?

DNA → mRNA → Protein → Trait.

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

Because it is the intermediary between DNA genetic code and proteins that perform cell functions

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

Used in mRNA vaccines, gene therapy, and CRISPR.

What makes RNA unstable?

It has ribose instead of deoxyribose

What is the ribose-phosphate backbone?

Sugar-phosphate chain forming RNA structure

What makes DNA more stable?

It’s backbone lacks one oxygen on each sugar

When does uracil pair with thymine?

Never, uracil pairs with adenine during protein synthesis

What are the three key differences between RNA and DNA?

Ribose vs deoxyribose, uracil vs thymine, single vs double strand.

What is messenger RNA?

Carries genetic coding from DNA to ribosomes to be used during transcription

What is a codon?

Three-base sequence coding for an amino acid.

What are amino acids?

The building blocks of proteins

What is an anticodon?

Three-base sequence complementary to codon, ensures correct amino acid is added during translation.

What do tRNA molecules do?

They are “adapters” that read genetic code on mRNA and deliver correct amino acids.

What does the cloverleaf shape of tRNA allow?

Binding to specific amino acids and complementary codons.

What is the small ribosomal subunit?

The smaller component of a ribosome, helps position mRNA and tRNA correctly.

What is the large ribosomal subunit?

Catalytic site for forming peptide bonds, connects amino acids together to form protein chains.

What do ribosomes do?

Matches mRNA codons to tRNA codons and links amino acids into polypeptide chains → functional proteins

Why is it important to understand transcription?

Because defects in it causes genetic disease.

What is RNA polymerase?

Catalyzes transcription.

Unwinds double helix, reads strand 3’ →5’. Synthesizes RNA 5’→3’ when it adds complementary ribonucelotides.

What is pre-mRNA?

Initial RNA transcript produced directly from DNA. Contains coding regions and non-coding regions

What are exons?

Coding regions of mRNA that will be kept

What are introns?

Noncoding regions of mRNA that will be removed

What is the 5’ cap?

Protects mRNA from degradation, required for ribosome binding and translation.

What is a Poly-A tail?

Added to the 3’ end of mRNA, protects mRNA from degradation and increases stability. Also helps with export and translation.

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

About 15%.

What is the ribosomal complex?

Molecular machine that reads mRNA and assembles proteins

During translation, what happens at initiation?

Ribosome assembles at start codon.

During translation, what happens to elongation?

The tRNA with complementary anticodon binds, amino acids are added to growing chain.

During translation, what happens at termination?

Stop codon recognized, completed polypeptide released

Why is gene regulation important?

It allows scientists to control when proteins are produced.

What is the regulator gene?

Encodes the repressor protein

What is the promoter region?

DNA binding site for RNA polymerase

What is the operator region?

Control switch for gene expression, also where the repressor protein binds to block transcription.

What is an inducer?

Binds to repressor and changes shape, preventing DNA binding.

What is the repressor protein?

Binds to operator region, blocking RNA polymerase. Prevents transcription.

What is the Tryptophan operon?

Reveals how bacteria manage amino acids synthesis.

What happens when tryptophan is absent?

Operon ON, enzymes made to synthesize tryptophan. Inducible gene expression

What happens when tryptophan is present?

Operon OFF, corepressor shuts down operon, enzymes not made. Negative feedback loop.

What is a point mutation?

Single base change.

Why is it important to understand point mutations?

Single base changes can have cascade effects throughout gene expression.

What is polymerase chain reaction?

Technique to amplify specific DNA sequences

How did PCR revolutionize medicine?

It enabled rapid testing, forensics, paternity testing, and detection of diseases from tiny samples.

What is the starting material for PCR?

Template DNA

What are PCR tubes?

Plastic tubes containing the reaction mixture

What are primers?

Short single-stranded DNA oligonucleotides

Where does the forward primer bind?

3’ end

Where does the reverse primer bind?

5’ end

What are deoxynucleotides?

Building blocks for new DNA synthesis.

What is Taq polymerase?

Synthesizes new DNA strands

Where is Taq polymerase isolated from?

Thermus aquaticus (bacteria in hot springs)

What does thermostable mean?

Survives repeated heating to 95 degrees without denaturing.

What are the three steps of PCR?

Denaturation, annealing, elongation.

What temperature does denaturation happen at?

95 degrees.

What happens during denaturation?

High temperature breaks hydrogen bonds, separates into two single strands.

What temperature does annealing happen at?

50-65 degrees