Genetics 3

Wild Type

Strain isolated from Nature

Mutation

Heritable change in the nucleotide sequence of an organism.

Mutant

Organism or a strain carrying a change in nucleotide sequence   compared to WT. 

Strain

Population of bacteria, yeast, etc. that derives from one ancestor.

base pair substitution

Mutation in which a single pair of bases in DNA is altered.   

Silent Mutation

Mutation that changes a nucleotide within a codon but does not change the corresponding amino acid.

nonsense Mutation

mutation that changes a nucleotide within a codon that results in a stop codon. 

missense Mutation

Mutation that changes a nucleotide within a codon that results in a change to the corresponding amino acid.

Frameshift Mutation

Mutation that alters the reading frame of a gene.

Base pair deletion

Removal of one or more nucleotide base pairs from DNA.

base pair insertion

Addition of one or more nucleotide base pairs into DNA.

duplication

A segment of DNA is copied, resulting in repeated sequences.

inversion

A segment of DNA is reversed in orientation within the chromosome.

Neutral Mutation

A mutation that has no effect on the organism’s fitness or phenotype.

Point mutation

A mutation affecting a single nucleotide (often a substitution).

Transition

A base substitution where a purine replaces a purine (A ↔ G) or a pyrimidine replaces a pyrimidine (C ↔ T).

Transversion

A base substitution where a purine is replaced by a pyrimidine or vice versa (A or G ↔ C or T).

Translocation

A segment of DNA is moved to a different location, often to another chromosome.

Physical Mutatants

mutants that show a visible change in appearance

• fruit flies altered eye color or wing shape

Auxotrophic Mutants

mutants that cannot synthesize a specific essential nutrient and must obtain it from the environment

• yeast that requires histidine added to the medium

• e coli mutant that cannot make tryptophan, must be grown on media with it

Conditional mutants

Mutants that show a phenotype only under certain conditions (restrictive conditions), but appear normal under others (permissive conditions).

• Temperature-sensitive mutant:

  • Protein works at 25°C (permissive)

  • Protein fails at 37°C (restrictive)

Resistance Mutants

Mutants that can survive exposure to substances that normally inhibit or kill cells.

• Bacteria resistant to antibiotics (e.g., ampicillin resistance)

Selectable Mutations

Mutations that give a growth advantage under certain conditions, allowing only mutants to survive.

• Antibiotic Resistance

Screenable Mutations

Mutations that do not affect survival, but can be visually or chemically distinguished.

• Color changes in colonies (blue vs. white screening)

Depurination

Spontaneous mutagen

• a purine base (A or G) is lost from DNA backbone leaving an abasic site

• DNAp might insert the wrong nucleotide or skip the site entirely

Deamination

Spontaneous Mutagen

• amino acid removed from base

• C>U

• changes base pairing properties, leads to point mutations during replication

Base analogs

Chemical mutagen

• resemble normal bases and are incorporated into DNA

• can pair incorrectly

• base substitutions occur during replication

Base-modifying agent

chemical mutagen

• alkylating agents alter structure of base

• causes mispairing

• cause point mutations

intercalating agents

chemical mutagen

• insert DNA base pairs

• distorts helix, causes DNAp to add or delete nucleotides

• causes frameshift mutations

UV radiation

physical mutagen

• causes formation of thymine dimers

• distorts DNA structure, blocking replication

• can cause incorrect base incorporations or replication erros

Depurination Definition

reaction where adenine or guanine is hydrolytically cleaved from sugar phosphate backbone of DNA, leaving an apurinic site, causing pro-mutagenic lesions that can cause DNA fragmentation or single-base deletions during replication

What chemicals cause depurination

acidic environments, high concentration of hydrogen ions

alkylating agents like dimethyl sulfate or nitrogen mustards

What effect does depurination have on the next round of replication

leads to stalling of DNAp with high mutagenic outcomes

Intercalating agent

chemical compound that inserts itself between stacked base pairs of DNAs double helix

• distorts DNA structure

What chemicals can intercalate

Ethidium bromide

acridine orange

proflavin

doxorubicin

actinomycin D

What kind of mutations do intercalating agents cause

1. Wedges between adjacent base pairs

2. this distorts DNA helix, disrupting normal DNA replication

3. DNA polymerase may insert an extra nucleotide or skip the nucleotide leading to a deletion

Explain why chemical mutagens only work on dividing cells.

Chemical mutagens primarily affect replicating DNA, as they interfere with the DNA synthesis process. This is because they target the cellular machinery that is active during cell division, leading to mutations in the newly synthesized DNA strands.

This process is caused by spontaneous hydrolysis of a glycosidic bond:

1. Depurination

2. Deamination

3. Both

4. Neither

a form of spontaneous mutation that results in the loss of a purine base from the DNA molecule, potentially leading to errors during DNA replication.

Depurination

This can happen to guanine but not cytosine:

1. Depurination

2. Deamination

3. Both

4. Neither

Depurination

This can happen to cytosine but not thymine:

1. Depurination

2. Deamination

3. Both

4. Neither

Deamination

Explain the essential features of transposons?

• transposons can jump from one DNA site to another

• they can encode an enzyme called transposase which recognizes the ends and catalyzes its movement

• they usually have inverted repeat sequences that are recognizes by transpsase

• 2 major types

  • DNA transposons

  • retrotransposons

explain how transposons cause mutations

Transposons are mobile DNA elements that cause mutations primarily by inserting into genes or regulatory regions, disrupting normal DNA sequence or gene expression, and by promoting chromosomal rearrangements through recombination between repeated sequences.

What is photoreactivation?

A DNA repair process that reverses UV-induced damage (specifically thymine dimers) using visible light.

What type of DNA damage does photoreactivation repair?

Thymine dimers caused by ultraviolet (UV) radiation.

hat enzyme is involved in photoreactivation?

DNA photolyase.

How is photolyase activated?

By exposure to visible light (blue light), which provides energy to break the thymine dimer bonds.

How does photoreactivation work (basic mechanism)?

Photolyase binds to the thymine dimer and uses light energy to split the abnormal bond, restoring normal DNA structure.

What organisms use photoreactivation?

Many bacteria, yeast, plants, and some animals.

Do humans (Homo sapiens) have photoreactivation?

No, humans do not have functional photoreactivation; we rely on other DNA repair systems like nucleotide excision repair.

What is nucleotide excision repair (NER)?

A DNA repair pathway that removes bulky, helix-distorting DNA damage (like thymine dimers) and replaces the damaged segment with new DNA.

What types of DNA damage does nucleotide excision repair fix?

Bulky lesions such as thymine dimers from UV light and chemical adducts that distort the DNA helix.

What are the basic steps of nucleotide excision repair?

• Damage recognition

• DNA unwinding around the lesion

• Dual incision (cutting out damaged strand segment)

• Removal of damaged oligonucleotide

• DNA synthesis to fill the gap

• DNA ligation to seal the strand

What enzyme complex carries out NER in bacteria?

The UvrABC endonuclease complex.

What enzyme complex is involved in NER in eukaryotes?

Multiple proteins including XPC (damage recognition), TFIIH (unwinding), endonucleases (XPF and XPG), DNA polymerase, and ligase.

How does the NER system “know” which strand to repair in bacteria?

It recognizes the methylation pattern—newly synthesized DNA is temporarily unmethylated, so the unmethylated strand is targeted for repair.

How does NER distinguish the damaged strand in eukaryotes?

It detects distortions in the DNA helix rather than relying on methylation; the damaged strand is identified by abnormal structure and stalled transcription/replication.

What recessive genetic disease results from defects in nucleotide excision repair?

Xeroderma pigmentosum (XP).

What is the main problem in xeroderma pigmentosum?

Cells cannot properly repair UV-induced DNA damage, leading to extreme sensitivity to sunlight and a high risk of skin cancer.

What is methyl-directed mismatch repair?

A DNA repair system that fixes base-pair mismatches and small insertion/deletion errors that occur after DNA replication.

When does mismatch repair occur?

Shortly after DNA replication, before the newly synthesized strand is fully modified or stabilized.

What is the first step of mismatch repair?

Mismatch recognition by proteins (MutS in bacteria) that detect incorrect base pairing.

What happens after mismatch recognition?

A repair complex (MutL and MutH in bacteria) is recruited to identify and cut the newly synthesized DNA strand near the mismatch.

How is the incorrect DNA segment removed in mismatch repair?

An exonuclease removes a stretch of nucleotides from the nick to past the mismatch.

How is the DNA repaired after removal of the mismatch?

DNA polymerase fills in the correct nucleotides using the original strand as a template, and DNA ligase seals the strand.

How do mismatch repair enzymes distinguish the “good” strand from the “mutated” strand in bacteria?

They use methylation patterns: the parental strand is methylated, while the newly synthesized strand is temporarily unmethylated.

Why is methylation important in mismatch repair?

It marks the original (correct) DNA strand, allowing the system to target the newly made strand for correction.

What enzyme introduces methylation in bacteria for strand discrimination?

DNA adenine methyltransferase (Dam methylase).

What is the key idea behind methyl-directed mismatch repair accuracy?

The system repairs the unmethylated (new) strand based on the methylated (original) template strand.

Is binary fission involved in asexual or sexual reproduction

Asexual reproduction

Is mitosis involved in asexual or sexual reproduction?

Asexual reproduction (used for growth, repair, and producing identical cells)

Is meiosis involved in asexual or sexual reproduction?

Sexual reproduction (produces gametes for reproduction)

Does binary fission occur in bacteria or eukaryotic cells?

Bacteria (prokaryotes)

Does mitosis occur in bacteria or eukaryotic cells?

Eukaryotic cells

Does meiosis occur in bacteria or eukaryotic cells?

Eukaryotic cells

What are homologous chromosomes?

Chromosomes that carry the same order of genes, although the two versions may differ slightly in base sequence.

What are sex chromosomes?

Chromosomes involved in determining whether an individual is male or female.

What is fertilization?

The union of sperm and egg during sexual reproduction.

What are chiasmata?

Connection points between homologous chromosomes produced by crossing over during prophase I of meiosis.

What is diploid?

A cell or organism with two sets of homologous chromosomes.

What is haploid?

A cell or organism with a single set of chromosomes.

What is a zygote?

A fertilized egg (diploid cell).

What is synapsis?

Pairing between homologous chromosomes during prophase I of meiosis where recombination occurs.

What are gametes?

Haploid cells in each parent that fuse together to form a diploid offspring.

What is gametogenesis?

The process of producing gametes.

What is a bivalent (tetrad)?

A pair of homologous chromosomes that have synapsed during meiosis I, containing four chromatids.

What is crossing over?

Exchange of DNA segments between homologous chromosomes.

What are eggs?

Female gametes; large, nutrient-rich, and non-motile.

Q: What are sperm?

A: Male gametes; small and often motile.

Q: What is the synaptonemal complex?

A: An elaborate protein structure that acts like a zipper, holding homologous chromosomes together during meiosis I.

Q: What is the difference between a sister chromatid and a chromosome?

A: A chromosome can be one DNA molecule (before replication) or two identical sister chromatids (after replication). Sister chromatids are identical copies of a single replicated chromosome joined at the centromere.

Q: What is the end result of mitosis?

A: Two genetically identical diploid daughter cells.

Q: What is the end result of meiosis?

A: Four genetically unique haploid gametes.

Q: What happens during prophase (mitosis)?

A: Chromosomes condense, nuclear envelope breaks down, spindle forms, and chromosomes prepare to align.

Q: What happens during metaphase (mitosis)?

A: Individual chromosomes line up at the metaphase plate.

Q: What happens during anaphase (mitosis)?

A: Sister chromatids separate and move to opposite poles.

Q: What happens during meiosis I?

A: Homologous chromosomes pair, cross over, and then separate into two haploid cells.

Q: What happens during meiosis II?

A: Sister chromatids separate, producing four haploid cells.

Q: Where does genetic diversity arise in meiosis?

A: Crossing over (prophase I) and independent assortment (metaphase I).

Q: How does metaphase of mitosis differ from metaphase I of meiosis?

A: Mitosis: single chromosomes line up. Meiosis I: homologous chromosome pairs (tetrads) line up.

Q: How does metaphase I differ from metaphase II of meiosis?

A: Metaphase I: homologous pairs align. Metaphase II: individual chromosomes (sister chromatids) align.