BIOSCI325: Genetics Exam 2

Missense Mutation

codon is changed to encode a different amino acid (AKA nonsynonymous)

Silent Mutation

codon is changed but encodes the same amino acid (AKA synonymous)

Nonsense Mutation

change of codon to STOP codon (UAG, UAA, UGA)

Frameshift Mutation

insertion or deletion of a number of nucleotides that isn’t a multiple of 3; every codon more 3’ is changed causing a shift in the reading frame

Substitution

one base pair in DNA sequence is replaced by another

Spontaneous Causes of Mutations

normal cellular conditions

Induced Causes of Mutations

external/environmental conditions

Mispairing

error made by DNA polymerase

What happens if mispairing isn’t corrected?

substitution

Strand Slippage

error made by DNA polymerase

What happens if strand slippage isn’t corrected?

single nucleotide insertion/deletion

Deamination

loss of an amine group from cytosine

What happens if deamination isn’t corrected?

substitution

Depurination

loss of purine base from nucleotide

What happens if depurination isn’t corrected?

substitution

Reversion

a second mutation that reverses the effects of a previous mutation (restores the original wild-type phenotype)

Ames Test

if a chemical causes mutations in DNA, it might also cause cancer

What are the spontaneous mutations?

mispairing, strand slippage, deamination, depurination

What DNA mutations can be corrected by a “back” mutation? How?

substitution and single nucleotide insertion and deletion; substitution reversion requires a second genetic mutation; single nucleotides insertion reversion requires the precise removal of the extra nucleotide that was inserted (opposite for single nucleotide deletion)

Neurospora crassa

a red bread mold used by Beadle and Tatum as a model organism because it is haploid and can grow on simple media

One Gene-One Enzyme Model

the theory that each gene is responsible for the production of a specific enzyme that catalyzes a single step in a metabolic pathway

Complete Media

nutrient-rich environment supplemented with all 20 amino acids and vitamins (it allows even mutated strains to survive)

Minimal Media

simple nutrient source containing only essential inorganic salts, a sugar (an energy source), and a vitamin (biotin)

Prototrophic

able to grow on minimal media; grows with just salts and sugar

Auxotrophic

unable to grow on minimal media (mutant phenotype)

Biosynthetic Pathways

a multi-step, enzyme-catalyzed series of reactions that convert simple starting materials into complex biological products

Precursor

the initial starting material in a pathway

Intermediate

compounds formed during the steps between the precursor and the final product

Product

the final compound produced by the pathway

Enzyme

a protein catalyst that speed sup a specific chemical reaction in the pathway

Sickle Cell Anemia

a landmark example in human genetics where a mutation in a single gene results in a change to hemoglobin

Beadle and Tatum’s Experiment

they proved that each gene is responsible for making one specific enzyme; if the gene is broken, that enzyme doesn’t get made, and the chemical step it controlled stops working

What mutation causes Sickle Cell Anemia?

sickle-cell anemia is caused by a missense (substitution at DNA level) mutation where GAG codon changes to GTG

Sugar-Utilizing

bacteria can produce a β-galactosidase and grow on lactose; it is able to consume and utilize sugar

Non-Utilizing

bacteria cannot metabolize lactose; it is unable to consume and utilize sugar

Gene Regulation

accounts for when and where a gene is transcribed

Operon

multiple proteins (LacZ, LacY, LacA) translated from one mRNA

Promoter (LacP)

binding site for RNA polymerase (non-coding; cis-acting)

Operator (LacO)

site where LacI binds (non-coding; cis-acting)

LacI

encodes LacI repressor protein, which binds to LacO (protein encoding; trans-acting)

CAP Site

DNA binding site for cAMP-CAP complex (non-encoding; cis-acting)

LacZ

encodes β-galactosidase, which breaks down lactose (protein-encoding; cis-acting)

LacY

encodes permease, transporting lactose into the cell

LacA

encodes Thiogalactoside transacetylase

LacI Repressor

the regulatory gene LacI produces; a protein that binds LacO

LacI Regulatory Domain

the part of the Lac repressor protein that binds allolactose to control gene expression

DNA-Binding Domain

an independently folded protein structure with a high affinity for specific or general DNA sequences

Catabolite Activator Protein (CAP)

activated by binding cAMP when glucose is low; binds the CAP site to facilitate RNA polymerase binding (positive regulation)

β-Galactosidase

enzyme that catalyzes the hydrolysis of lactose into glucose and galactose, as well as breaking down allolactose

X-Gal Blue/White Assay

used in molecular cloning; active β-galactosidase (blue = β-Gal present/Lac genes ON; white = β-Gal absent/Lac genes OFF) breaks down X-Gal

trans-acting

factors that diffuse and act on genes at different DNAs (proteins)

cis-acting

factors that only influence genes on the same DNA (DNA elements like the promoter)

Lactose

a sugar that only wild-type E. Coli can consume

Allolactose

the “signal” molecule that binds to the Lac repressor, allowing for gene expression

Glucose

the molecule that binds to CAP and activates transcription

cAMP (Cyclic AMP)

binds with CAP to form a positive-regulator molecule

Constitutive Expression

continuous, unregulated expression of genes

Constitutive Mutant

operon is always “ON”, regardless of lactose presence (LacI^- and LacO^c)

Super-Repressor Mutant

repressor can’t bind allolactose; open is never on

Negative Regulation

repressor bound to operator prevents transcription (default)

Positive Regulation

CAP-cAMP binds to promoter, enabling transcription

Activator Protein

transcription factors that increase gene expression by binding to specific DNA sequences and promoting RNA polymerase activity

No Lactose, + Glucose

LacI is bound to LacO; LacI wins, no transcription

No Lactose, No Glucose

LacI is still bound to LacO; LacI wins, no transcription

+ Lactose, + Glucose

Allolactose is present so LacI can’t bind DNA; LacI not bound, weak expression possible

+ Lactose, No Glucose

Allolactose is present so LacI can’t bind DNA; CAP protein bound to CAP site (positive regulation)

Wild-Type E. Coli in Presence/Absence of Lactose (Blue/White)

w/ lactose = white; w/o lactose = blue

LacZ^- Mutant in Presence/Absence of Lactose (Blue/White)

w/ and w/o lactose = white

LacI^- Mutant in Presence/Absence of Lactose (Blue/White)

w/ and w/o lactose = blue

LacO^c Mutant in Presence/Absence of Lactose

w/ and w/o lactose = blue

LacP^- Mutant in Presence/Absence of Lactose

w/ and w/o lactose = white

LacI^s Mutant in Presence/Absence of Lactose

w/ and w/o lactose = white

LacZ^- Mutant

LacZ gene is completely missing (no β-galactosidase encoded; lactose can’t be broken down)

LacP^- Mutant

prevents RNA polymerase from binding (transcription can’t happen)

LacO^c Mutant

prevents LacI binding from binding to operator (LacI repressor protein can’t win, transcription keeps happening)

LacI^- Mutant

LacI gene is completely missing (repressor protein can’t be synthesized, transcription keeps happening)

LacI^s Mutant

prevents LacI from binding allolactose (LacI repressor protein wins, transcription can’t happen)

Chromatin

a complex of DNA and protein that forms chromosomes within the nucleus

Condensation

the process of packing DNA into a more compact, dense structure

Histones

small, positively charged proteins (H2A, H2B, H3, H4 in each layer) that acts as spools around which DNA wraps

Nucleosomes

the fundamental building blocks of protein (1 nucleosome = 8 histones)

Euchromatin

lightly packed, open form of chromatin; transcription is active

Heterochromatin

highly condensed, tightly packed form of chromatin; inactive transcription

Histone Acetylation

the addition of acetyl groups to lysine residues on histone tails

DNA Methylation

the covalent addition of methyl groups, usually to cytosine residues

RNA Interference (RNAi)

a mechanism that relies on RNA-RNA complementarity to control the amount of an mRNA

Double-Stranded RNA (dsRNA)

a molecule with 2 complementary strands, which acts as a trigger for RNAi

Short Interfering RNA (siRNA)

small 21 nucleotide (19-22) double-stranded RNA fragments derived from the cleavage of long-double stranded RNA; they have 3’ overhangs on each side

RNA-Induced Silencing Complex (RISC)

unzips the double-stranded RNA and uses siRNA to recognize which strand to keep and which to degrade

Micro RNA (miRNA)

short, 21-22 nucleotide, single-stranded RNA with 3’ overhangs

Effect of Histone Acetylation on Transcription

histone acetylation loosens chromatin, boosting transcription

Effect of DNA Methylation on Transcription

DNA methylation represses gene transcription by blocking transcription factors from binding; promotes tightly packed, inactive chromatin structure (heterochromatin)

Characteristics of siRNA

double-stranded (dsRNA), perfectly complementary to target mRNA, usually acts on a single target, often dervied from exogenous degredation

Characteristics of miRNA

endogenous, transcribed from cellular DNA, possesses loop structures, binds with partial complementarity to the 3’ UTR of multiple mRNAs

Fire and Mello’s Experiment Conditions

three conditions: injecting sense RNA, antisense RNA, and dsRNA (most effective)

Double-Stranded Break

a severe form of DNA damage where both strands are severed

Ionizing Radiation

high-energy waves/particles that can detach electrons, causing double-stranded breaks and oxidative damage

Ultraviolet Radiation

non-ionizing radiation that causes “bulky” damage and strand slippage

Thymine Dimer

a bulky lesion formed when two adjacent thymine bases on the same DNA strand become covalently linked to UV radiation, distorting the DNA helix

Mutagen

a physical/chemical agent that permanently changes genetic material