Molecular Genetics Practice Flashcards

Comprehensive vocabulary flashcards covering genetic variation, molecular markers, DNA enzymes, PCR, cloning, transcription, translation, and historical genetics experiments.

Student Staff Liaison Committee (SSLC)

A committee for first-year LabMed students to provide course feedback, requiring attendance four times a year for about an hour, comprising approximately 18 students plus staff.

Polymorphism

A genetic variation that continues to exist throughout a population and is passed down from generation to generation.

Continuous Variation

Phenotypic variation that is hard to measure directly and influenced by multiple genes and environmental factors, such as human height.

Discontinuous Variation

Phenotypic variation controlled by one or a few genes resulting in distinct categorical traits, such as fly wing structures or coat color.

Conserved Core Genes

Genomic regions highly conserved across diverse species (e.g., human, rhesus monkey, dog, mouse, chicken, zebrafish) that encode essential traits like vision, cardiovascular systems, and growth.

Selective Breeding

The practice of repeatedly breeding selected parent organisms over generations to maximize desired traits for commercial gain, such as larger fish, larger corn, or white alpacas.

Green Fluorescent Protein (GFP)

A protein originally isolated from jellyfish that glows under UV light, used experimentally as a tracking tool for protein movement and cancer treatment monitoring.

Peppered Moth Industrial Melanism

An evolutionary shift in British peppered moth populations from predominantly white ($90\%$) to dark grey/black after 1900 due to soot from the Industrial Revolution covering tree bark.

Genetic Drift

Random changes in population allele frequencies caused by chance events, such as accidental crushing or selective predation.

Bottleneck Effect

A sharp reduction in population size and genetic redundancy due to environmental pressures or human activity, seen in Australian eucalypt dominance and Cavendish bananas.

Founder Effect

A loss of genetic variation occurring when a small isolated sub-population establishes a new population, causing genetic divergence over generations.

Hardy-Weinberg Principle

A mathematical principle stating that genotype and allele frequencies remain constant over generations assuming random mating, unbiased selection, no mutation, no migration, and a large population.

Allele Frequency Formula

The mathematical ratio defined as the number of copies of a given allele divided by the total number of alleles present in the population.

Single Nucleotide Variation (SNV) / SNP

A genetic variation occurring as a change in a single base pair in the DNA sequence.

Cri du Chat Syndrome

A structural chromosomal variation resulting from a deletion of the terminal tail end of chromosome $5$.

Klinefelter's Syndrome

A chromosomal variation characterized by an $XXY$ karyotype, tall stature, reduced muscle tone, and adult infertility.

Patau Syndrome

A chromosomal disorder caused by trisomy $13$, presenting with microcephaly, cardiac failure, polydactyly, and failure to thrive.

Turner's Syndrome

A chromosomal variation characterized by an $XO$ karyotype, short stature, delayed puberty, skeletal issues, and horseshoe kidneys.

Transition Mutation

A point mutation where a purine base is swapped for another purine, or a pyrimidine is swapped for another pyrimidine.

Transversion Mutation

A point mutation where a purine base is replaced by a pyrimidine base, or vice versa.

Nonsense Mutation

A point mutation that creates a premature stop codon, terminating protein synthesis early.

Missense Mutation

A point mutation that substitutes a single base to alter an amino acid codon, resulting in an altered protein product.

Thalassemia

An inherited anemia caused by mutations in alpha- or beta-globulin genes, leading to reduced hemoglobin production and lower oxygen transport capacity.

Codominant Marker

A molecular marker where the heterozygous genotype displays traits from both homozygous parent alleles.

Non-epistatic Marker

A genetic marker whose expression is independent and not controlled or modified by another gene.

Minisatellites (VNTRs)

Variable Number Tandem Repeats consisting of non-coding repeating sequences $15\text{ to }70\,bp$ in length, spanning up to $5\,kb$, used in original DNA fingerprinting.

Microsatellites (STRs)

Short Tandem Repeats consisting of repeating DNA motifs $2\text{ to }6\,bp$ in length, spanning less than $300\,bp$, widely used for forensic PCR testing.

ABO Blood Group Genetics

A blood group locus on chromosome $9$ with codominant $A$ and $B$ alleles and deletion-mutation $O$ alleles resulting in non-functional surface proteins.

Sickle Cell Heterozygote Advantage

A point mutation changing glutamic acid to valine in hemoglobin ($Hb^S$) where heterozygotes ($Hb^S Hb^A$) resist malarial parasite reproduction in red blood cells.

Phosphodiester Bond Hydrolysis

The enzymatic breaking of the bond between the $3'\text{-hydroxyl}$ group and $5'\text{-phosphate}$ group of adjacent nucleotides by nucleases.

Ethylenediaminetetraacetic Acid (EDTA)

A chelating agent used during DNA extraction to sequester divalent metal cofactors like $Mg^{2+}$, thereby inactivating nucleases.

DNase I

An endonuclease from bovine pancreas that cleaves single- or double-stranded DNA into di-, tri-, and tetranucleotides, producing nicks with $Mg^{2+}$ or cuts with $Mn^{2+}$.

Exonuclease III

An E. coli exonuclease that sequentially removes nucleotides from the $3'\text{-terminus}$ of double-stranded DNA with blunt ends or $5'\text{-overhangs}$.

S1 Nuclease

An exonuclease from Aspergillus that selectively cleaves single-stranded DNA and RNA, used to trim single-stranded overhangs or loop structures.

Restriction Endonuclease

A bacterial enzyme that recognizes foreign bacteriophage DNA sequences and cleaves internal phosphodiester bonds as a defense mechanism.

Bacterial Restriction-Modification System

A bacterial defense mechanism combining a restriction endonuclease that cleaves foreign unmethylated DNA and a methylase that methylates host DNA.

Palindromic Recognition Site

A DNA sequence that reads identically in the $5'\text{ to }3'$ direction on both complementary strands, such as $5'\text{-GAATTC-}3'$.

Type II Restriction Enzymes

Predictable restriction endonucleases that cleave within or adjacent to palindromic recognition sites ($4\text{ to }8\,bp$), generating sticky or blunt ends without requiring ATP.

Sticky Ends (Cohesive Ends)

Single-stranded $5'$ or $3'$ overhangs generated by staggered restriction enzyme cuts, capable of re-attaching via hydrogen bonding.

T4 DNA Ligase

An enzyme that catalyzes phosphodiester bond formation between adjacent $5'\text{-phosphate}$ and $3'\text{-hydroxyl}$ ends in DNA using ATP.

Proofreading Activity ($3'\text{ to }5'$ Exonuclease)

A DNA polymerase catalytic activity that removes mispaired nucleotides from the $3'\text{-end}$ during replication to minimize errors.

Klenow Fragment

The large fragment of E. coli DNA Polymerase I lacking the $5'\text{ to }3'$ exonuclease subunit, retaining $5'\text{ to }3'$ polymerase and $3'\text{ to }5'$ proofreading activities.

Terminal Transferase

A template-independent DNA polymerase that adds random or specified nucleotides to the $3'\text{-end}$ of DNA using cobalt as a cofactor.

Kary Mullis

The scientist who invented Polymerase Chain Reaction (PCR) in 1985 using thermal-stable DNA polymerase, winning the Nobel Prize in 1993.

PCR Denaturation Step

The phase in PCR where double-stranded DNA is heated to $95\text{--}98^\circ\text{C}$ to break hydrogen bonds and separate it into single strands.

PCR Primer Annealing Step

The phase in PCR where reaction temperature is dropped to allow short oligonucleotide primers to hybridize to complementary target sequences.

PCR Primer Melting Temperature Formula

An estimation formula calculated as $T_m = 4 \times (G + C) + 2 \times (A + T)^\circ\text{C}$, with annealing temperature set at $T_m - 5^\circ\text{C}$.

Heated Lid (PCR Thermal Cycler)

A cycler component maintained above block temperature to prevent reaction liquid from vaporizing and condensing inside tube caps.

No-Template Control (Water Blank)

A PCR control tube containing all reaction components except template DNA, used to verify the absence of reagent or laboratory aerosol contamination.

Complementary DNA (cDNA)

Synthetic double-stranded DNA produced from a single-stranded messenger RNA template using reverse transcriptase.

Reverse Transcriptase

An enzyme that uses an RNA template to synthesize a complementary single-stranded DNA molecule.

RNase H

An enzyme that selectively degrades the RNA strand within RNA-DNA heteroduplexes during cDNA preparation.

Plasmid Vector Essentials

The three essential structural features of a cloning vector: an origin of replication (ori), a selectable marker, and a multiple cloning site (MCS).

Multiple Cloning Site (MCS)

A short region engineered inside a cloning vector that contains unique recognition sites for multiple restriction endonucleases.

Vector Dephosphorylation

The removal of $5'\text{-phosphate}$ groups from linearized vector ends to prevent self-ligation prior to insert ligation.

Bacterial Transformation Efficiency

A measurement yielding approximately $10^6\text{ transformants/}\mu\text{g}$ DNA using calcium chloride heat-shock and $10^{10}\text{ transformants/}\mu\text{g}$ DNA using electroporation.

Genomic Library

A collection of recombinant clones containing DNA fragments that collectively represent an organism's entire genome.

cDNA Library

A collection of cloned cDNA fragments representing only the mRNA transcripts expressed in a specific cell or tissue sample at a given time.

Blue/White Selection (LacZ Screening)

A screening technique where DNA insertion into the lacZ alpha-fragment gene disrupts beta-galactosidase production, resulting in white recombinant colonies.

Central Dogma of Molecular Biology

The molecular framework encompassing DNA replication, transcription of DNA into RNA, and translation of RNA into protein.

Ribose vs Deoxyribose

RNA contains ribose sugar with a $2'\text{-hydroxyl}$ group ($-\text{OH}$), while DNA contains deoxyribose lacking an oxygen atom at carbon $2'$.

Uracil

A pyrimidine nitrogenous base in RNA that pairs with adenine via two hydrogen bonds, substituting for thymine.

Transcription Start Site ($+1$ Position)

The exact DNA nucleotide location corresponding to the first nucleotide incorporated into a newly synthesized RNA transcript.

Bacterial Promoter Consensus Sequences

Conserved DNA regions located upstream of bacterial start sites at $-10$ (Pribnow box, $5'\text{-TATAAT-}3'$) and $-35$ ($5'\text{-TTGACA-}3'$).

RNA Polymerase Holoenzyme

The functional bacterial transcription complex comprising the core RNA polymerase enzyme and a sigma ($\sigma$) factor.

Sigma Factor ($\sigma$)

A bacterial RNA polymerase subunit required for promoter recognition, such as $\sigma^{70}$ for general genes and $\sigma^{32}$ for $42^\circ\text{C}$ heat-shock stress genes.

Template Strand (Antisense Strand)

The DNA strand read by RNA polymerase in the $3'\text{ to }5'$ direction to synthesize RNA in the $5'\text{ to }3'$ direction.

Coding Strand (Sense Strand)

The non-template DNA strand ($5'\text{ to }3'$) matching the sequence of the synthesized RNA transcript, except containing thymine instead of uracil.

Rho-Dependent Termination

Transcription termination where the Rho protein tracks along new RNA and unwinds the RNA-DNA hybrid when RNA polymerase pauses at a GC-rich region.

Rho-Independent (Intrinsic) Termination

Termination driven by a GC-rich inverted repeat in RNA that folds into a hairpin loop followed by a poly-U tract, pulling the RNA transcript out.

Eukaryotic RNA Polymerases

Nuclear RNA polymerases where Pol I makes large rRNA, Pol II makes mRNA and snRNA, and Pol III makes small rRNA ($5\text{S}$) and tRNA.

TATA Box

A eukaryotic core promoter sequence located $-25\text{ to }-30\,bp$ upstream of the start site, bound by TATA-binding protein (TBP).

Eukaryotic $5'$ Cap

A $7$-methylguanosine cap added to the $5'\text{-end}$ of pre-mRNA via a $5'\text{--}5'$ triphosphate linkage to protect mRNA and facilitate ribosome binding.

Poly-A Tail

A tract of adenine residues added to the $3'\text{-end}$ of eukaryotic pre-mRNA by poly-A polymerase following cleavage at a $5'\text{-AAUAAA-}3'$ signal.

Exons

Coding regions of pre-mRNA retained in mature mRNA transcripts after splicing to encode protein sequences.

Introns

Non-coding intervening sequences in pre-mRNA excised by the spliceosome during mRNA processing.

Spliceosome

A complex of small nuclear RNAs (snRNAs) and proteins that removes pre-mRNA introns via a lariat loop structure and splices exons together.

Dystrophin Gene Scale

A human gene spanning $2.5 \times 10^6\,bp$ of pre-mRNA ($99\%$ introns) that is spliced down to a mature $1.4 \times 10^4\,bp$ mRNA.

Codon

A sequence of three consecutive mRNA nucleotides specifying a single amino acid or translation stop signal.

Start Codon

The mRNA codon $5'\text{-AUG-}3'$ that initiates translation and specifies methionine.

Stop Codons

The three mRNA codons ($5'\text{-UAA-}3'$, $5'\text{-UAG-}3'$, $5'\text{-UGA-}3'$) that signal translation termination via release factors.

Transfer RNA (tRNA) Structure

An adapter RNA with a cloverleaf secondary structure, a $3'\text{-CCA}$ amino acid attachment site, modified bases, and an anticodon loop.

Aminoacyl-tRNA Synthetase

An enzyme that attaches a specific amino acid to the $3'\text{-end}$ of its corresponding tRNA molecule using ATP.

Prokaryotic Ribosome Subunits ($70\text{S}$)

A bacterial ribosome consisting of a $50\text{S}$ large subunit ($23\text{S}$ and $5\text{S}$ rRNAs) and a $30\text{S}$ small subunit ($16\text{S}$ rRNA).

Eukaryotic Ribosome Subunits ($80\text{S}$)

A eukaryotic ribosome consisting of a $60\text{S}$ large subunit ($28\text{S}, 5.8\text{S}, 5\text{S}$ rRNAs) and a $40\text{S}$ small subunit ($18\text{S}$ rRNA).

Shine-Dalgarno Sequence

A purine-rich bacterial mRNA sequence upstream of the AUG start codon that base-pairs with $16\text{S}$ rRNA in the $30\text{S}$ ribosomal subunit to position initiation.

Kozak Sequence

A eukaryotic mRNA consensus sequence ($5'\text{-ACCAUGG-}3'$) surrounding the AUG start codon that facilitates ribosome recognition.

Ribosomal A, P, and E Sites

The Aminoacyl (A) site accepts incoming charged tRNA, the Peptidyl (P) site holds tRNA with the growing peptide, and the Exit (E) site releases uncharged tRNA.

Wobble Hypothesis

Crick's hypothesis explaining that flexible base pairing at the $3'$ position of an mRNA codon ($5'$ position of anticodon) allows 32 tRNAs to read 61 codons.

Polycistronic mRNA

An mRNA transcript carrying coding sequences for multiple proteins expressed from a single bacterial operon promoter.

Operon

A bacterial genetic unit comprising multiple genes controlled by a single promoter and operator, producing polycistronic mRNA.

Griffith's Transformation Experiment (1928)

An experiment showing that mixing live rough avirulent (Type II-R) Pneumococcus with heat-killed smooth virulent (Type III-S) bacteria transformed R cells into live S cells.

Avery, MacLeod, and McCarty Experiment (1944)

An experiment proving DNA is the transforming principle by showing transformation occurs unless DNA is degraded by DNase.

Hershey-Chase Blender Experiment (1952)

An experiment using T2 phage labeled with $^{35}\text{S}$ (protein) and $^{32}\text{P}$ (DNA) showing that $^{32}\text{P}$ enters bacteria to direct viral replication.

Watson and Crick Double Helix Model (1953)

The double-stranded antiparallel model of DNA with external sugar-phosphate backbones and internal complementary base pairing.

Rosalind Franklin's Photo 51

An X-ray diffraction image of B-DNA showing a clear cross pattern that proved the helical structure of DNA.

Chargaff's Rules

Empirical rules stating that in double-stranded DNA, adenine equals thymine ($\text{A}=\text{T}$) and guanine equals cytosine ($\text{G}=\text{C}$).

Purines vs Pyrimidines

Purines (adenine, guanine) are double-ring bases, while pyrimidines (cytosine, thymine, uracil) are single-ring bases.

Hydrogen Bonding in DNA Base Pairs

Adenine pairs with thymine via two hydrogen bonds ($\text{A}=\text{T}$), while guanine pairs with cytosine via three hydrogen bonds ($\text{G}\equiv\text{C}$).

Meselson-Stahl Experiment (1958)

An experiment using $^{15}\text{N}$ and $^{14}\text{N}$ isotopes in $\text{CsCl}$ density gradients proving DNA replicates semi-conservatively.