PCB3036 - Exam 3 Study Guide

DNA Repair

Cellular processes that detect and correct damage to DNA, maintaining genetic stability. Examples include excision repair and mismatch repair.

Mnemonic: Fix the script - DNA's repair kit!

Category of Transponsons

Transposons can be DNA-only (cut and paste), retrotransposons (use RNA intermediate), or replicative (copy and move)

Mnemonic: DNA jumps, RNA copies, and both can cause floppies!

Bacteria as a Model Organism

Bacteria like E. coli are used for genetic studies due to fast reproduction, simple genome, and ease of manipulation.

Mnemonic: E. coli a star in the lab car!

Mutation

A change in DNA sequence that may affect protein function or gene regulation. Can be spontaneous or induced.

Mnemonic: Mutation = DNA's typo station

RNA Viruses

Viruses with RNA as genetic material, often have high mutation rates (ex. HIV, influenza)

Mnemonic: RNA viruses mutate away, keeping vaccines at bay!

DNA Repair Mechanism

Specific pathways like base excision repair, nucleotide excision repair, and mismatch repair correct different types of DNA damage.

Mnemonic: NER, BER, and MMR, DNA's damage repair stars!

Novel Phenotype

A new observable trait that appears due to a mutation or genetic interaction, not seen in parents.

Mnemonic: It's novel, it's neat, a genetic twist you meet!

Phage T4

A lytic bacteriophage that infects E. coli, often used to study DNA replication and repair.

Mnemonic: T4 = kill door, it lyses E. coli galore!

Replicative Transposition

A transposon is copied, and the copy inserts elsewhere in the genome, increasing copy number.

Mnemonic: Copy and paste, DNA get laced!

Point Mutation

A single base change in DNA; can be silent, missense, or nonsense.

Mnemonic: One dot, big plot!

Phage Lambda

A temperate bacteriophage that can choose between a lytic (burst) and lysogenic (hide) life cycle in E. coli.

Mnemonic: Lambda’s a chooser, be a breaker (lytic) or snoozer (lysogenic)!

Mismatch Repair Pathway

A DNA repair process that fixes incorrect base pairings after DNA replication, using the old strand as the correct template.

Mnemonic: Mismatch? No match! Let's patch!

Mutation Types

Includes point mutations (single base changes), insertions, deletions, and larger chromosomal changes.

Mnemonic: Points, pops, and flips, mutation takes trips!

T4 DNA

The double stranded DNA genome of phage T4; it's linear and has modified bases that protect it from host restriction enzymes.

Mnemonic: T4's tricky DNA, modified to keep attackers at bay!

Retrotransposition

A type of transposition where the element is transcribed into RNA, then reverse transcribed into DNA and inserted elsewhere.

Mnemonic: Retro = RNA first, then DNA reverse burst!

Forward Mutation

A mutation that changes a wild type allele to a mutant form.

Mnemonic: Forward = from normal to abnormal.

Excision Repair

A repair process that cuts out and replaces damaged DNA segments (includes base- and nucleotide-excision repair).

Mnemonic: Excise the slice, make DNA nice!

Phage Lambda Cycle

Refers to the two possible cycles: lytic (host lysis) or lysogenic (viral DNA integrates into host genome).

Mnemonic: Lambda's fork: smash or stash!

Cut and Paste Transposition

A DNA transposon is excised from one location and inserted into another, without copying itself.

Mnemonic: Cut it here, paste it there!

Reverse Mutation (Back Mutation)

A mutation that restores the original wild type phenotype, either by fixing the original mutation or compensating for it.

Mnemonic: Reverse it, rehearse it, go back to the original verse!

Lysogenic Pathway

Viral DNA integrates into the host genome and lies dormant as a prophage, replicating with the host until triggered to enter the lytic cycle.

Mnemonic: Lysogenic = lazy guest virus!

Bacillus Subtilis (B. subtilis)

A model Gram-positive bacterium used in genetic studies; known for forming endospores and competence in DNA uptake.

Mnemonic: B. subtilis, spore forming, smart little studious bug!

Mismatched Base Pairing

Occurs when non-complementary nucleotides pair up (e.g., A-C or G-T), often leading to mutations if not repaired.

Mnemonic: Bad dating: G went with T, Mismatch alert!

F Factor

A plasmid that enables bacteria to form a sex pilus and transfer DNA during conjugation; found in E. coli.

Mnemonic: F = Fertility = Flirty factor!

Holliday Model

A model for homologous recombination where two DNA molecules exchange strands, forming a Holliday junction.

Mnemonic: Holliday junction = DNA dance party!

Episome

A genetic element, like a plasmid, that can exist independently or integrate into the host chromosome (ex.F factor).

Mnemonic: Epi = extra, and it sticks if it wants!

Transposition

The movement of DNA sequences (transposons) from one genomic location to another.

Mnemonic: Transposons = DNA's little travelers!

Hemoglobin S

A mutant form of hemoglobin found in individuals with sickle cell disease, caused by a missense mutation (Glu → Val).

Mnemonic: S = Sickle; one swap makes cells sickle!

IS Elements (Insertion Sequences)

Simple transposons that carry only the genes needed for transposition, like transposase.

Mnemonic: IS = It Slides!

Null Alleles

Mutated alleles that produce no functional product, often caused by deletions or nonsense mutations.

Mnemonic: Null = Nothing made!

Uni- and Bi- directional Replication

DNA replication can proceed in one (uni-) or both (bi-) directions from an origin of replication.

Mnemonic: One way street or two lane road for DNA copying!

HIV Mechanism

HIV is a retrovirus that uses reverse transcriptase to convert its RNA into DNA, integrating into the host genome.

Mnemonic: HIV rewinds: RNA → DNA → trouble!

Bacterial Chromosome

A single circular DNA molecule that contains most of the bacterial genome.

Mnemonic: Bacteria like rings, one big looped gene thing!

Tn5

A well studied composite transposon that carries antibiotic resistance genes and uses cut and paste transposition.

Mnemonic: Tn5 cuts deep and resists the meds!

Lethal Mutations

Mutations that cause death of the organism, usually by disrupting essential genes.

Mnemonic: Lethal = Life ends!

Auxotrophs

Mutants that require additional nutrients for growth because they've lost the ability to synthesize them.

Mnemonic: Auxo = Oops! I can't make my own!

Tn3

A composite transposon that replicates itself (replicative transposition) and often carries antibiotic resistance.

Mnemonic: Tn3 makes three: it copies itself with glee!

Tautomeric

Tautomeric shifts are rare, spontaneous changes in base structure that cause mispairing during replication.

Mnemonic: Tautomer twist = base pair miss!

Prototrophs

Wild type bacteria that can synthesize all required nutrients and grow on minimal media.

Mnemonic: Proto = Pro at growing solo!

Cut and Paste Transposons

Move by being excised and inserted into a new location, no copy made.

Mnemonic: Cut here, paste there. Gone from square one!

Base Pair Combinations

The standard pairings are A-T and G-C in DNA (or A-U in RNA).

Mnemonic: A loves T, G hugs C!

Antibiotics / r and Amino Acid +/-

Antibiotic resistance (r) means bacteria can grow in the presence of antibiotics.

Amino Acid +/- refers to whether a strain can synthesize (+) or requires supplementation (−).

Mnemonic: r = resistant rebel; + means self-sufficient, − needs a supplement!

Ds Element

A non autonomous maize transposon that requires the Ac (Activator) element to move.

Mnemonic: Ds = Dependent slider, needs Ac to ride!

Tautomeric Shift

A spontaneous change in a DNA base's form that leads to incorrect base pairing and possible mutations.

Mnemonic: Tautomer twist makes a mispair tryst!

Plasmids

Small, circular DNA molecules in bacteria that replicate independently and can carry useful genes like antibiotic resistance.

Mnemonic: Plasmid = portable power disk!

Rolling Circle Replication

A replication method where one DNA strand rolls out while being copied, common in plasmids and viruses.

Mnemonic: Like a fruit roll-up, unroll to copy!

Base Pair Substitutions

A mutation where one nucleotide base is swapped for another; can be silent, missense, or nonsense.

Mnemonic: One switch, three glitch flavors!

Monoploid

An organism or cell with one set of chromosomes, common in bacteria and gametes.

Mnemonic: Mono = one, and done!

IS Elements Sequence

Insertion sequences contain inverted repeats and the transposase gene key components for "cut and paste" transposition.

Mnemonic: IS = It Slices with repeats and tools!

Mutagenic Agents

Physical or chemical agents that cause mutations, like UV light, radiation, or chemicals.

Mnemonic: Mutagens = DNA mischief-makers!

Recombination

The process of exchanging genetic material between DNA molecules, important in meiosis and repair. Essential for genetic diversity!

Mnemonic: Recombination = remixing DNA hits!

Retrovirus like Elements

Transposons that resemble retroviruses, using reverse transcription to move (ex. LINEs in humans).

Mnemonic: Retro-style jumpers, RNA to DNA to genome!

Acridine Dyes

Mutagenic chemicals that intercalate into DNA, causing frameshift mutations.

Mnemonic: Acrid dyes slide in and mess the lines!

DNA Transport

Movement of DNA into a cell, such as during transformation.

Mnemonic: Mail delivery: DNA edition!

L1 Elements

Long Interspersed Nuclear Elements (LINEs), a type of retrotransposon in the human genome.

Mnemonic: L1 = Long and Lazy—copy/paste specialists!

Radiation Inducing Mutations

UV or ionizing radiation causes DNA damage like thymine dimers or double strand breaks.

Mutation: Radiation = rip and zap DNA!

DNase and Transformation

DNase destroys free DNA; adding it during transformation prevents DNA uptake by bacteria.

Mnemonic: DNase = transformation eraser!

Transposons Orientation

The direction of transposon insertion can affect gene expression depending on promoter or coding region disruption.

Mnemonic: Flip it wrong, turn genes off!

Bacteria Transductant

A bacterium that has received DNA via transduction, which is transfer by a virus (phage).

Mnemonic: Transductant = virus delivery customer!

HIV Infection

HIV enters host cells, reverse transcribes RNA into DNA, and integrates into the genome using LTRs.

Mnemonic: HIV rewinds to hide inside!

Bruce Ames

Created the Ames Test to detect chemical mutagens using bacteria and mutation rates.

Mnemonic: Ames aims for mutagens!

DNA Repair Enzymes

Include nucleases, polymerases, and ligases that cut out damage, fill gaps, and seal DNA.

Mnemonic: Cut, patch, seal, DNA repair wheel!

UV Light

Causes thymine dimers, blocking replication and transcription if unrepaired.

Mnemonic: UV = sunburn for your genes!

Spontaneous Mutations

Natural mutations that occur due to replication errors or molecular instability.

Mnemonic: Oops! Nature's glitch!

E. Coli

A model bacterium used in genetics for plasmid transformation, transduction, and cloning.

Mnemonic: E. coli = the lab's favorite pet bug!

S. Aureus

A Gram positive bacterium known for antibiotic resistance (ex. MRSA).

Mnemonic: S. aureus = stubborn staph survivor!

C. Elegans

A tiny nematode used in genetics and development studies due to its simple, mapped genome.

Mnemonic: C. elegans = elegant model worm!

Prophage

Dormant phage DNA integrated into a bacterial genome during the lysogenic cycle.

Mnemonic: Prophage = sleeping virus page!

Att B Site

The specific bacterial DNA site where phage lambda integrates its DNA during lysogeny.

Mnemonic: Att B = where lambda parks its DNA!

Point Mutant

An organism with a single base change mutation in its DNA.

Mnemonic: One point, one plot twist!

Lysogenic Life Cycle

Phage DNA integrates and replicates silently with the host until activated.

Mnemonic: Lysogenic = long nap in the genome!

Adaptive Mutation

The idea that some mutations arise in response to environmental stress, not random (still debated).

Mnemonic: Adapt and mutate, react to your fate!

Composite Transposons

Complex transposons with genes flanked by IS elements, often carrying antibiotic resistance.

Mnemonic: Two ISs, one gene stash!

HFR (High-Frequency Recombination)

A bacterial cell with the F factor integrated into its chromosome, leading to frequent gene transfer during conjugation.

Mnemonic: HFR = gene-sharing superstar!

Suppressor Mutation

A mutation that hides or cancels the effect of another mutation, restoring function or phenotype.

Mnemonic: Suppress the mess!

The Central DOGMA (DNA → RNA → Protein)

Everything begins with DNA. Cells need to copy, use, and protect their DNA.

Replication copies DNA:

Uses DNA polymerase and follows either uni- or bi-directional replication.

Bacteria (like E. coli) replicate circular chromosomes using rolling circle replication in plasmids.

Mismatch repair, excision repair, and DNA repair enzymes fix mistakes during or after replication.

If not fixed, spontaneous mutations (like point mutations, base-pair substitutions, or tautomeric shifts) can occur.

Mnemonic: Mutation is the typo, repair is the editor

Bacteria As Models

Bacteria (like E. coli and B. subtilis) are genetic powerhouses:

They're monoploid (one chromosome), so mutations have immediate effects.

Plasmids are small DNA circles with genes (e.g., antibiotic resistance).

The F factor is a plasmid that helps bacteria conjugate (share DNA).

If F integrates into the chromosome, the cell becomes an HFR strain (shares genes at high frequency).

Prototrophs can grow on minimal media; auxotrophs need nutrients due to mutations.

Mutagenic agents (UV, radiation, acridine dyes) induce mutations to study gene function.

Mnemonic: Bacteria are genetic test tubes with turbo-charged DNA sharing.

How DNA Moves

DNA isn't stationary. It moves, especially in microbes and viruses.

1. Transposons - "Jumping Genes"

IS elements and composite transposons (Tn3, Tn5) move within the genome.

Movement types:

Cut and paste (physically moves)

Replicative transposition (copy and insert elsewhere)

Retrotransposition (RNA → DNA → inserted, like L1 elements or retrovirus-like elements)

Transposons can disrupt genes, cause lethal mutations, or lead to novel phenotypes.

Orientation matters—if inserted wrong, gene expression changes.

Mnemonic: Transposons = DNA travelers, sometimes troublemakers.

Viruses & Phages - Hijacking the System

A. Bacteriophages (Phage T4, Lambda)

T4 is strictly lytic - infects, copies, and bursts the host.

Lambda can choose:

Lytic: active infection → host lysis.

Lysogenic: integrates into host genome at attB site as a prophage.

Prophage DNA can later "wake up" and become lytic again.

B. HIV (a retrovirus)

Infects human cells and uses reverse transcriptase to go from RNA → DNA.

The viral DNA integrates into the host genome with help from LTRs (long terminal repeats).

This is a form of retrotransposition.

Mnemonic: Viruses write their story into your DNA script.

Mutations - Change the Story

Mutations are central to everything in genetics.

Point mutations, insertions, or deletions lead to:

Forward mutations (wild-type → mutant)

Reverse mutations (mutant → wild-type)

Suppressor mutations (second mutation that fixes the first)

Null alleles produce no product; lethal mutations kill the organism.

Adaptive mutations may occur in response to stress (controversial idea).

Mnemonic: Mutation: the fuel of evolution, and sometimes disaster.

Genetic Tools & Tests

These tools help researchers understand genes:

Ames test (Bruce Ames): Uses bacteria to detect chemical mutagens.

Transformation: Uptake of DNA from environment.

Blocked by DNase (chews DNA).

Transduction: Virus-mediated DNA transfer.

A bacterium that receives DNA = transductant.

Mnemonic: Transformation, transduction, conjugation, bacteria's DNA swap meet!

How It All Connects

DNA → Replication → Mutation (natural or induced)

↓

DNA Repair (Mismatch, Excision, Enzymes)

↓

Transposons + Viruses Move DNA → Disrupt genes → Create variation

↓

Mutations → Novel traits, disease, resistance

↓

Bacteria share DNA via plasmids, phages, or uptake

↓

Scientists manipulate this system (Ames test, transformation)

In An Organism Like E. Coli

1. Starts with a circular chromosome (monoploid) + maybe a plasmid (like the F factor).

2. Can undergo mutation (e.g., point mutation → auxotroph).

3. Can repair damage (MMR, excision).

4. May have transposons moving around the genome.

5. Can be infected by phage T4 or Lambda, entering lytic or lysogenic cycles.

6. Can share DNA via conjugation (F factor), transformation (DNA uptake), or transduction (phage).

7. Used in labs to test mutagens, insert genes, or study gene function.