Biology 30 - Molecular Genetics: DNA Structure, Replication, and Gene Expression

Comprehensive practice flashcards covering molecular genetics, historical discovery of DNA as the hereditary material, DNA structure, replication enzymes and mechanisms, as well as transcription, RNA processing, and translation.

Hämmerling's Experiments

Reciprocal grafting and regeneration experiments using the single-celled alga Acetabularia (divided into cap, stalk, and rhizoid) demonstrating that the cell's hereditary information is contained within the nucleus.

Griffith's Experiments

Experiments involving the injection of pathogenic and non-pathogenic strains of Streptococcus pneumoniae into mice, showing that a heat-killed virulent strain transferred genetic material to a live harmless strain, demonstrating transformation.

Transformation

The uptake and incorporation of foreign extracellular DNA fragments into a bacterial chromosome, altering the recipient bacterium's genotype and phenotype.

Hershey-Chase Experiment

An experiment using T2 bacteriophages with radioactively labeled proteins ($^{35}\text{S}$) and DNA ($^{32}\text{P}$) to infect bacterial cells, conclusively proving that DNA—not protein—is the hereditary genetic material.

Purines

A class of double-ringed nitrogenous bases found in nucleic acids, consisting of adenine (A) and guanine (G).

Pyrimidines

A class of single-ringed nitrogenous bases found in nucleic acids, consisting of cytosine (C), thymine (T), and uracil (U).

Chargaff's Rule

The principle stating that in a double-stranded DNA sample, the percentage of adenine equals thymine ($\%A = \%T$) and the percentage of guanine equals cytosine ($\%G = \%C$).

Rosalind Franklin

The scientist whose pioneering X-ray diffraction photograph of DNA (Photo 51) provided critical evidence that DNA has a helical structure.

Watson and Crick

The scientists who deduced the double-helix model of DNA structure in 1953 and received the Nobel Prize in 1962 alongside Maurice Wilkins.

Anti-parallel

The orientation of the two complementary strands of a DNA double helix, which run parallel to each other but in opposite chemical directions ($5'$ to $3'$ and $3'$ to $5'$).

Semi-Conservative Replication

The mechanism of DNA duplication demonstrated by Meselson and Stahl wherein each of the two parental strands separates and serves as a template, producing daughter double helices composed of one parental strand and one newly synthesized strand.

DNA Helicase

The replication enzyme that unwinds the double helix and unzips parental DNA strands at the replication fork by breaking hydrogen bonds between base pairs.

Topoisomerase

An enzyme that relieves supercoiling tension and prevents overwinding of the DNA double helix ahead of the replication fork.

Primase

An enzyme that synthesizes short complementary RNA primers on single-stranded template DNA to provide a free $3'\text{-OH}$ group for DNA polymerase to begin synthesis.

DNA Polymerase III

The primary enzyme in replication that synthesizes new complementary DNA strands in the $5'$ to $3'$ direction by adding free nucleotides starting at RNA primers, while also proofreading mistakes.

Leading Strand

The continuously synthesized DNA strand that is elongated non-stop toward the replication fork in the $5'$ to $3'$ direction.

Lagging Strand

The discontinuously synthesized DNA strand that is elongated away from the replication fork in short Okazaki fragments using multiple RNA primers.

Okazaki Fragments

Short stretches of newly synthesized DNA separated by RNA primers formed discontinuously on the lagging template strand.

DNA Polymerase I

The enzyme that removes RNA primer sequences from newly synthesized DNA strands and fills the resulting gaps with appropriate DNA nucleotides.

DNA Ligase

The enzyme that joins adjacent Okazaki fragments and DNA strands together by creating phosphodiester bonds along the sugar-phosphate backbone.

Replication Bubble

An unwound region along a chromosome formed by two replication forks traveling in opposite directions, allowing replication to occur simultaneously at multiple sites.

Transcription

The enzymatic synthesis of a complementary mRNA molecule from a DNA template strand, carried out in the nucleus by RNA Polymerase in the $5'$ to $3'$ direction.

Translation

The protein synthesis stage occurring in the cytoplasm where ribosomes decode the nucleotide sequence of mRNA into a specific polypeptide chain.

Promoter

A specific regulatory DNA sequence located at the beginning of a gene that is recognized and bound by RNA Polymerase to initiate transcription.

Template Strand

The anti-sense strand of DNA that RNA Polymerase reads to build a complementary single-stranded mRNA molecule.

Messenger RNA (mRNA)

The single-stranded RNA transcript that carries genetic instructions encoded in codons from nuclear DNA to ribosomes in the cytoplasm.

Transfer RNA (tRNA)

A specialized RNA adaptor that ferries specific amino acids to the ribosome, containing a triplet anticodon complementary to an mRNA codon.

Ribosomal RNA (rRNA)

The structural and catalytic RNA component that combines with proteins to construct ribosomes and catalyzes peptide bond formation during translation.

Codon

A triplet sequence of adjacent nucleotides in mRNA that specifies a single amino acid or signals the initiation or termination of protein synthesis.

Anticodon

A sequence of three nucleotides on a tRNA molecule that forms complementary base pairs with a corresponding codon on an mRNA transcript.

AUG

The universal initiator start codon on mRNA that specifies the amino acid methionine and establishes the reading frame for translation.

Terminator Codons

The three stop codons on mRNA (UAA, UAG, and UGA) that do not code for amino acids and instead signal release factors to end translation.

Introns

Non-coding intervening sequences of eukaryotic pre-mRNA transcripts that are removed and degraded before mRNA is transported to the cytoplasm.

Exons

The coding expressed sequences of eukaryotic pre-mRNA that are retained and spliced together to form mature mRNA translated into proteins.

Spliceosome

A molecular machine in eukaryotic nuclei that removes non-coding introns from pre-mRNA and splices the exons together prior to translation.

Differences between RNA and DNA

1. Strands: RNA is single-stranded ($1$ strand), whereas DNA is double-stranded ($2$ strands). 2. Sugar: RNA contains ribose sugar, whereas DNA contains deoxyribose sugar. 3. Bases: RNA contains uracil ($\text{U}$) instead of thymine ($\text{T}$); both share adenine ($\text{A}$), cytosine ($\text{C}$), and guanine ($\text{G}$).

Differences between RNA and DNA

1. Strands: RNA is single-stranded ($1$ strand), whereas DNA is double-stranded ($2$ strands). 2. Sugar: RNA contains ribose sugar, whereas DNA contains deoxyribose sugar. 3. Bases: RNA contains uracil ($\text{U}$) instead of thymine ($\text{T}$); both share adenine ($\text{A}$), cytosine ($\text{C}$), and guanine ($\text{G}$).

What is a mutation?

permanent change in the genetic material of an organism.

What are the two cell types in which mutations can occur?

Somatic cells and germ cells.

What are somatic cell mutations?

Mutations in non-sex cells. They are not passed to the next generation but can lead to cancer.

What are germ cell mutations?

Mutations in sex cells (sperm or egg). They can be passed on to future generations and affect the offspring.

What are the two possible effects of mutations on a population?

Beneficial mutations can increase in a population over time. Harmful mutations may be selected against by natural selection.

What are spontaneous mutations?

Mutations caused by mistakes made by DNA polymerase I or III.

What can spontaneous mutations produce?

Different alleles, which are different versions of a gene.

What are induced mutations?

Mutations caused by mutagens.

What are four examples of mutagens?

UV light, X-rays, chemicals, and some viruses.

What is the relationship between mutations and cancer?

Scientists agree that cancers are related to mutations.

How can a mutation affect a protein?

A change in the DNA sequence can change the amino acid sequence, which can affect the protein's folding, shape, and function.

What is the BRCA-1 example from the slides?

Women carrying the genetic variation described in the slides are seven times more likely to get breast cancer.

What is the cystic fibrosis example from the slides?

Missing three nucleotides (CTT) at a specific location is associated with cystic fibrosis.

What is a point mutation?

A mutation that affects only one base pair.

What is a substitution mutation?

One base is replaced by another base.

What is a silent mutation?

A substitution that still codes for the same amino acid.

What is a missense mutation?

A substitution that codes for a different amino acid.

What is a nonsense mutation?

A mutation that creates a stop codon, ending protein production early.

What is a deletion mutation?

One or more nucleotides are removed from the DNA sequence.

What is an insertion mutation?

One or more nucleotides are added to the DNA sequence.

What is a frameshift mutation?

An insertion or deletion that changes the reading frame and therefore changes subsequent codons.

Why are frameshift mutations usually harmful?

They can change many subsequent codons and produce a completely different protein. The slides note that they usually result in nonsense mutations.

How does deleting one letter illustrate a frameshift mutation?

Deleting a letter changes how the remaining letters are grouped into three-letter words, similar to how a deletion changes codon groupings.

Can a frameshift mutation ever be beneficial?

Rarely. It can sometimes produce a new beneficial trait and increase genetic variability.

What happens if a mutation occurs in a sperm or egg cell?

The mutation can be passed on to the embryo and be present in every cell of the resulting organism.

What is polymerase chain reaction (PCR)?

A technique used to make copies of a specific DNA sequence.

What is gene cloning?

Using bacteria to create copies of a gene for isolation.

What is the difference between PCR and gene cloning?

PCR copies a specific DNA sequence. Gene cloning uses bacteria to create copies of a gene for isolation.

What is gel electrophoresis?

A technique used to separate pieces of DNA based on their size.

What two things does gel electrophoresis use?

An agarose gel and an electric current.

When can gel electrophoresis be used in biotechnology?

After DNA has been cut with restriction enzymes.

What is another use of gel electrophoresis?

DNA fingerprinting, also called DNA profiling.

What is DNA fingerprinting?

A technique that compares DNA patterns to help distinguish between individuals.

What are VNTRs?

Variable Number Tandem Repeats found in non-coding sections of DNA.

What does tandem repeat mean?

A DNA sequence repeated side by side.

Why are VNTRs useful in DNA fingerprinting?

Different people can have different numbers of repeats.

What does the example of eight tandem repeats represent?

Eight side-by-side repeats of the same four-nucleotide sequence.

What are STRs?

Short tandem repeats. The slides show STRs at different DNA locations and compare the number of repeats among people.

How can DNA fingerprinting help determine paternity?

DNA patterns can be compared between a child and potential biological parents.

How can DNA fingerprinting help solve crimes?

DNA patterns from a sample can be compared with samples from different people.

What is Penta D in the DNA fingerprinting example?

An STR name shown in the slides.

What does D16 refer to in the slides?

An STR on chromosome 16.

What does the number of repeats show in DNA profiling?

The number of times a particular DNA sequence repeats at a specific location.

What is mitochondrial DNA (mtDNA)?

DNA found in mitochondria. Mitochondria have their own DNA.

Where is mitochondrial DNA found?

The slides state that mtDNA is found in all organisms.

How is mitochondrial DNA inherited?

It is passed down from the mother through the egg.

Why is mtDNA usually inherited from the mother?

The egg supplies the mitochondria, while the sperm contributes its nucleus.

What are four uses of mitochondrial DNA?

Studying evolutionary history through the maternal line, maternity testing, disaster victim identification, and cold-case forensics.

Why is mtDNA useful for studying evolutionary history?

It can be used to trace the maternal line.