Molecular Biology: DNA, RNA, Proteins, and Chromatin Structure

What is molecular biology?

Molecular biology studies biological processes at the level of DNA, RNA, and proteins.

What are the central macromolecules of life?

DNA, RNA, and proteins.

What is the Central Dogma of molecular biology?

Genetic information flows from DNA → RNA → Protein.

What does DNA store?

DNA stores genetic information.

What is RNA's role in the cell?

RNA acts as an intermediate between DNA and protein and can have structural or catalytic roles.

What do proteins do?

Proteins perform most cellular functions, including catalysis, structure, signaling, and transport.

What is genotype?

Genotype is the genetic information encoded in DNA.

What is phenotype?

Phenotype is the observable traits produced by gene expression.

Why is structure important in molecular biology?

Structure determines function at the molecular level.

What is a nucleotide?

A nucleotide consists of a nitrogenous base, a sugar, and one or more phosphate groups.

What is a nucleoside?

A nucleoside is a nitrogenous base plus a sugar.

What sugars are found in DNA and RNA?

DNA contains deoxyribose; RNA contains ribose.

What bases are purines?

Adenine (A) and guanine (G).

What bases are pyrimidines?

Cytosine (C), thymine (T), and uracil (U).

How are nucleotides linked together?

By phosphodiester bonds between the 5′ phosphate and 3′ hydroxyl groups.

Why does DNA have directionality?

Because nucleotides are linked 5′ to 3′, giving each strand polarity.

How do DNA strands pair?

Through complementary base pairing via hydrogen bonds (A-T, G-C).

Why is GC-rich DNA more stable?

G-C pairs form three hydrogen bonds instead of two.

What is B-DNA?

The most common right-handed DNA helix found in cells.

What is A-DNA?

A shorter, wider right-handed helix often found in RNA-DNA hybrids.

What is Z-DNA?

A left-handed DNA helix associated with high salt or supercoiling.

What are major and minor grooves?

Unequal grooves in DNA that allow protein binding and sequence recognition.

What is DNA supercoiling?

The overwinding or underwinding of DNA.

What is negative supercoiling?

Underwound DNA that facilitates strand separation.

What is positive supercoiling?

Overwound DNA that resists strand separation.

What do topoisomerases do?

They relieve torsional strain by cutting and rejoining DNA.

How does RNA differ from DNA?

RNA has ribose sugar, uracil instead of thymine, and is usually single-stranded.

Why is RNA less stable than DNA?

The 2′-OH group in ribose makes RNA more chemically reactive.

What is mRNA?

Messenger RNA carries coding information from DNA to ribosomes.

What is tRNA?

Transfer RNA delivers amino acids to the ribosome during translation.

What is rRNA?

Ribosomal RNA forms the structural and catalytic core of ribosomes.

What are RNA secondary structures?

Structures like hairpins formed by intramolecular base pairing.

What is a ribozyme?

An RNA molecule with catalytic activity.

What is the RNA world hypothesis?

The idea that early life relied on RNA for both information storage and catalysis.

What is a codon?

A three-nucleotide RNA sequence that specifies an amino acid.

What is an open reading frame (ORF)?

A continuous stretch of codons that begins with a start codon and ends with a stop codon.

What is primary protein structure?

The linear sequence of amino acids.

What is secondary protein structure?

Local folding into α-helices and β-sheets stabilized by hydrogen bonds.

What is tertiary structure?

The full three-dimensional folding of a protein.

What is quaternary structure?

The assembly of multiple protein subunits.

What determines protein function?

Amino acid sequence and three-dimensional structure.

What are DNA-binding domains?

Protein motifs that recognize specific DNA sequences.

What is a zinc finger?

A DNA-binding motif stabilized by zinc ions.

What is a helix-turn-helix motif?

A common DNA-binding structure in transcription factors.

What is chromatin?

Chromatin is the complex of DNA and proteins that packages eukaryotic DNA inside the nucleus.

Why is DNA packaged into chromatin?

Packaging compacts DNA and regulates access to genetic information.

What is a histone?

Histones are basic proteins that DNA wraps around to form chromatin.

Which histones make up the core nucleosome?

Two copies each of H2A, H2B, H3, and H4.

What is histone H1?

A linker histone that binds DNA between nucleosomes and promotes higher-order structure.

What is a nucleosome?

A nucleosome consists of ~147 bp of DNA wrapped around a histone octamer.

What is linker DNA?

DNA between nucleosomes that varies in length.

What is the 'beads-on-a-string' structure?

The 10-nm fiber formed by nucleosomes connected by linker DNA.

What is the 30-nm fiber?

A more compact chromatin structure formed by folding of nucleosomes.

Are higher-order chromatin structures static?

No, chromatin structure is dynamic and regulated.

What is euchromatin?

Loosely packed, transcriptionally active chromatin.

What is heterochromatin?

Densely packed, transcriptionally inactive chromatin.

What is constitutive heterochromatin?

Permanently condensed chromatin (e.g., centromeres, telomeres).

What is facultative heterochromatin?

Chromatin that can switch between active and inactive states.

What are histone tails?

Flexible N-terminal regions of histones that are chemically modified.

What is histone acetylation?

Addition of acetyl groups to lysines, reducing histone-DNA interactions.

What effect does acetylation have on transcription?

It generally increases transcription.

What enzyme adds acetyl groups?

Histone acetyltransferases (HATs).

What enzyme removes acetyl groups?

Histone deacetylases (HDACs).

What is histone methylation?

Addition of methyl groups to histone tails.

Does histone methylation always repress transcription?

No, it can activate or repress depending on the residue modified.

What is the histone code hypothesis?

The idea that combinations of histone modifications specify chromatin function.

How is the histone code interpreted?

By proteins that recognize specific modifications.

What is a bromodomain?

A protein domain that binds acetylated histones.

What is a chromodomain?

A protein domain that binds methylated histones.

What are chromatin remodeling complexes?

ATP-dependent complexes that reposition or remove nucleosomes.

Why are chromatin remodelers important?

They regulate DNA accessibility for transcription, replication, and repair.

What are restriction enzymes?

Restriction enzymes are bacterial endonucleases that cut DNA at specific sequences.

Why do bacteria have restriction enzymes?

They protect bacteria from foreign DNA such as bacteriophages.

What is a restriction site?

A specific DNA sequence recognized and cut by a restriction enzyme.

What are palindromic sequences?

DNA sequences that read the same 5′→3′ on both strands.

What are sticky ends?

DNA ends with single-stranded overhangs that can base-pair with complementary sequences.

What are blunt ends?

DNA ends with no overhangs.

What does DNA ligase do?

DNA ligase forms phosphodiester bonds to join DNA fragments.

Why are sticky ends useful for cloning?

They increase ligation efficiency by base-pairing before ligation.

What is a plasmid?

A small, circular DNA molecule that replicates independently of the chromosome.

What is an origin of replication (ori)?

A sequence that allows plasmid replication in host cells.

What is a selectable marker?

A gene (often antibiotic resistance) used to identify transformed cells.

What is PCR?

PCR is a method to exponentially amplify a specific DNA sequence.

What enzyme is used in PCR?

A heat-stable DNA polymerase (e.g., Taq polymerase).

What are the three steps of PCR?

Denaturation, annealing, and extension.

Why are primers required in PCR?

DNA polymerases require a 3′-OH group to begin synthesis.

What is reverse transcription?

The synthesis of DNA from an RNA template.

What enzyme performs reverse transcription?

Reverse transcriptase.

What is agarose gel electrophoresis?

A method to separate DNA fragments by size using an electric field.

How do DNA fragments move in a gel?

Smaller fragments migrate faster than larger ones.

What is qPCR used for?

Measuring the amount of DNA or RNA in real time.

What is Ct value?

The cycle number at which fluorescence exceeds background levels.

What is SYBR Green?

A dye that fluoresces when bound to double-stranded DNA.

What is a TaqMan probe?

A sequence-specific fluorescent probe used in qPCR.

What does NanoDrop measure?

DNA concentration using absorbance.

What does Qubit measure?

DNA concentration using fluorescence for higher specificity.

What is Sanger sequencing?

A sequencing method using chain-terminating dideoxynucleotides.

What are ddNTPs?

Nucleotides lacking a 3′-OH that terminate DNA synthesis.

What is Illumina sequencing?

A next-generation sequencing method based on sequencing by synthesis.

What is Oxford Nanopore sequencing?

A long-read sequencing method detecting electrical changes as DNA passes through a pore.