MCB 1310: Comprehensive Molecular Biology, Biotechnology, and Forensics

Comprehensive vocabulary flashcards covering proteins, proteomics, DNA replication, PCR technologies, forensic molecular biology (STR and probability analysis), and gene therapy/CRISPR editing.

Proteome

The entire, dynamic set of proteins expressed by an organism, cell, or tissue at a specific time under designated environmental and physiological conditions.

Proteomics

The scientific discipline dedicated to studying the complete protein complement of cells and tissues, comparing healthy and diseased states to discover diagnostic biomarkers and targeted drug candidates.

Amino Acid

The monomer building block of proteins consisting of a central alpha ($\alpha$) carbon bonded to an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), a hydrogen atom, and a variable side chain ($R$ group) that confers unique chemical properties.

Peptide Bond

A covalent bond formed between the carboxyl carbon of one amino acid and the amino nitrogen of another via a condensation (dehydration synthesis) reaction, releasing a molecule of $\text{H}_2\text{O}$.

Primary Structure

The unique, linear sequence of amino acids joined together by covalent peptide bonds in a polypeptide chain.

Secondary Structure

Localized, repetitive folding patterns of a polypeptide backbone—most notably $\alpha$-helices and $\beta$-pleated sheets—stabilized by hydrogen bonds between amino and carbonyl groups.

Tertiary Structure

The overall three-dimensional conformation of a single folded polypeptide chain, determined by interactions among variable $R$ group side chains and the surrounding aqueous solvent.

Quaternary Structure

The multi-subunit spatial arrangement formed when two or more distinct polypeptide chains bond together into a single functional protein complex.

Chymosin (Prochymosin)

An enzyme produced from calf stomach cells (or expressed recombinantly in microorganisms from cloned cDNA) that cleaves casein in milk to form cheese curd.

High-Performance Liquid Chromatography (HPLC)

An analytical chromatography method that forces a liquid solvent carrying proteins through a matrix-packed column under high pressure, often coupled to mass spectrometry for protein identification.

SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis)

A vertical electrophoretic technique that uses heat and the anionic detergent SDS to denature proteins and coat them with a uniform negative charge, separating them through polyacrylamide gel pores strictly by molecular weight.

Western Blot

An analytical procedure in which proteins separated by SDS-PAGE are transferred via electric current onto a nitrocellulose or PVDF membrane and identified using target-specific antibodies.

Primary Antibody

In an immunoassay or Western blot, an antibody that specifically recognizes and binds directly to the target protein antigen immobilized on the membrane.

Secondary Antibody

In a Western blot, an antibody that recognizes the host species of the primary antibody and carries a conjugated reporter enzyme (such as alkaline phosphatase or HRP) that reacts with a substrate to produce a visible signal.

Semiconservative Replication

The biological mechanism of DNA synthesis wherein each daughter DNA double helix consists of one conserved original parental strand and one newly synthesized complementary strand.

Origin of Replication (Ori)

A specific sequence along a DNA molecule where helicase initiates unwinding and replication machinery begins synthesizing new strands bidirectionally.

Replisome

The comprehensive molecular machine and multi-enzyme complex located at the replication fork that coordinates the enzymes and proteins needed for DNA synthesis.

Replication Fork

The Y-shaped junction formed when double-stranded parental DNA is unwound and separated into two single strands by helicase.

DNA Helicase

The replication enzyme that moves along double-stranded DNA and separates the two strands by breaking the hydrogen bonds between complementary base pairs.

Topoisomerase (DNA Gyrase)

An enzyme that acts ahead of the replication fork to relieve torsional strain and prevent excessive supercoiling of the parental double helix during unwinding.

Single-Stranded Binding Proteins (SSBs)

Proteins that bind to exposed single-stranded template DNA to prevent the parental strands from premature re-annealing and reforming a double helix.

DNA Primase

An RNA polymerase enzyme that synthesizes short RNA primers ($10\text{--}15$ nucleotides long) complementary to template DNA, establishing free $3'\text{-OH}$ attachment points for DNA polymerase.

DNA Polymerase III

The primary prokaryotic replication enzyme that catalyzes phosphodiester bond formation between incoming dNTPs and the free $3'\text{-OH}$ group of a growing strand, elongating DNA strictly in the $5' \rightarrow 3'$ direction.

Okazaki Fragments

Short, discontinuous segments of newly synthesized DNA formed on the lagging strand template as DNA polymerase synthesizes away from the opening replication fork.

DNA Polymerase I

The enzyme responsible for removing RNA primer nucleotides from Okazaki fragments and filling the resulting gaps with complementary DNA nucleotides.

DNA Ligase

An enzyme that catalyzes the formation of a phosphodiester bond between adjacent Okazaki fragments, sealing nicks in the sugar-phosphate backbone into a continuous strand.

Telomerase

A ribonucleoprotein enzyme present in eukaryotic stem cells and cancer cells that uses an intrinsic RNA template to extend repetitive chromosome ends, overcoming the end-replication problem.

Polymerase Chain Reaction (PCR)

An in vitro technique discovered by Kary B. Mullis (Nobel Prize in Chemistry in 1993) that rapidly amplifies a specific target DNA sequence millions of times through repetitive thermal cycling.

Thermal Cycler (Thermocycler)

An automated laboratory instrument programmed to rapidly cycle reaction tubes through specific temperatures for the denaturation, annealing, and extension steps of PCR.

Taq DNA Polymerase

A heat-stable DNA polymerase isolated from the thermophilic archaeon/bacterium Thermus aquaticus that resists thermal denaturation at $94\text{--}96\,^\circ\text{C}$ during PCR cycling.

Denaturation (PCR)

The initial phase of a PCR cycle in which high heat ($94\text{--}96\,^\circ\text{C}$) breaks hydrogen bonds between base pairs, converting double-stranded template DNA into single strands.

Annealing (PCR)

The second phase of a PCR cycle ($55\text{--}65\,^\circ\text{C}$) in which forward and reverse single-stranded oligonucleotide primers ($20\text{--}30\text{ bp}$) bind to complementary sequences flanking the target region.

Extension (PCR)

The third phase of a PCR cycle ($70\text{--}75\,^\circ\text{C}$, typically $72\,^\circ\text{C}$) where Taq polymerase adds dNTPs to the $3'$ ends of primers to synthesize complementary DNA strands.

Reverse Transcription PCR (RT-PCR)

A biological technique that utilizes reverse transcriptase to convert isolated mRNA into complementary DNA (cDNA), which is then amplified via PCR to determine if a specific gene is actively transcribed.

cDNA (Complementary DNA)

A DNA copy synthesized from a messenger RNA template by reverse transcriptase that represents only the expressed, exon-derived protein-coding portion of a gene.

Quantitative Reverse Transcriptase PCR (qRT-PCR)

A real-time variation of RT-PCR that quantifies gene expression levels during thermal cycling by monitoring fluorescence emitted from double-stranded DNA-binding dyes or probes.

GAPDH

A constitutively expressed housekeeping gene used as an internal positive control in RT-PCR to verify proper RNA extraction, reverse transcription, and amplification across all tested lanes.

Restriction Fragment Length Polymorphism (RFLP)

A forensic profiling method developed by Alec Jeffreys in 1984 that uses restriction enzymes to cut intact genomic DNA into fragments at specific sites, separating VNTR-containing fragments by agarose gel electrophoresis.

Variable Number Tandem Repeats (VNTRs)

Repetitive, non-coding genomic sequences consisting of tandem repeating units between $1$ and $100\text{ bp}$ long, characterized by high size polymorphism among individuals.

Short Tandem Repeats (STRs)

Short tandem repeating units of $2\text{--}10\text{ bp}$ dispersed evenly throughout non-coding nuclear DNA that are amplified via PCR and serve as the modern standard for forensic identity testing.

Agarose Gel Electrophoresis

A method using an electric field to drive negatively charged nucleic acids through a galactose-based red algae matrix toward the positive anode, separating fragments strictly by base-pair length.

Capillary Electrophoresis

An automated separation method in which fluorescently labeled STR products migrate through narrow, polymer-filled capillary tubes past a laser detector, generating an electropherogram of signal peaks.

Electropherogram

A computer-generated graph showing relative fluorescence detected over time during capillary electrophoresis, with individual alleles displayed as colored peaks indicating fragment size and repeat count.

CODIS (Combined DNA Index System)

The FBI's nationwide forensic DNA database launched in October 1998, which expanded its required core STR marker battery from $13$ loci to $20$ loci effective January 1, 2017.

Amelogenin (AMEL) Locus

A gender-identification marker residing on both the X and Y chromosomes; females exhibit a single peak ($\text{XX}$) due to identical length alleles, whereas males exhibit two distinct peaks ($\text{XY}$).

Multiplex PCR

A PCR reaction that combines multiple distinct, fluorescently labeled primer sets in a single tube to amplify up to $20$ different STR loci simultaneously from small biological samples.

Mitochondrial DNA (mtDNA) Typing

A rigorous forensic technique analyzing the $37$-gene circular mitochondrial genome inherited exclusively from the maternal lineage, utilized primarily when nuclear DNA is degraded or absent.

Ex Vivo Gene Therapy

A genetic therapy approach in which cells are harvested from a patient, genetically modified or corrected in cell culture, and subsequently reinfused into the patient's body.

In Vivo Gene Therapy

A therapeutic strategy in which gene-carrying vectors are administered or injected directly into the target organs or tissues within a patient's living body.

Viral Vector

A replication-deficient, genetically modified virus (such as Adeno-Associated Virus, Lentivirus, or Retrovirus) engineered to deliver therapeutic genetic sequences into human host cells.

Liposome

A small, artificial hollow sphere formed from a lipid bilayer used as a non-viral vector to package and deliver therapeutic genes or antisense molecules across cell membranes.

Antisense RNA Technology

A gene-silencing strategy where a single-stranded RNA molecule complementary to a target mRNA is delivered, base-pairing with the transcript to physically block its translation by ribosomes.

RNA Interference (RNAi)

A cellular post-transcriptional gene-silencing pathway in which double-stranded RNA is processed into short fragments that direct the degradation of complementary mRNA molecules.

Dicer

An endoribonuclease enzyme in the RNAi pathway that cleaves long double-stranded RNA molecules into small interfering RNAs (siRNAs) approximately $21$ nucleotides in length.

RISC (RNA-Induced Silencing Complex)

A cytoplasmic multi-protein complex that incorporates single-stranded siRNAs to identify, bind, and cleave target cellular mRNA transcripts, preventing protein translation.

CRISPR-Cas9

A genome-editing system adapted from bacterial adaptive immunity consisting of the Cas9 endonuclease and a single guide RNA (sgRNA) that introduces targeted double-strand breaks into DNA.

Single Guide RNA (sgRNA)

A synthetic RNA molecule engineered with a nucleotide sequence complementary to a specific genomic target, directing the Cas9 enzyme to the precise site intended for cleavage.

Protospacer Adjacent Motif (PAM)

A short, conserved DNA sequence located immediately adjacent to the target genomic site that is strictly required for the Cas9 endonuclease to recognize, bind, and cut DNA.

Sickle Cell Disease (HBB Mutation)

A genetic disorder caused by a single-nucleotide missense mutation ($\text{A} \rightarrow \text{T}$) in the HBB gene on chromosome 11, changing glutamic acid to valine ($\text{Glu} \rightarrow \text{Val}$) and producing abnormal hemoglobin S (HbS).

Adenosine Deaminase (ADA) Deficiency (SCID)

A severe combined immunodeficiency caused by defects in the ADA gene that lead to toxic dATP accumulation in T cells, successfully treated in 1990 in the first approved human ex vivo retroviral gene therapy trial.

Leber's Congenital Amaurosis (LCA)

An inherited degenerative retinal condition caused by defects in the RPE65 gene, treated by in vivo subretinal injection of an adeno-associated virus (AAV) vector carrying normal RPE65.

Jesse Gelsinger

An 18-year-old patient who died in 1999 during an OTC deficiency clinical trial due to a systemic inflammatory immune response to a high-dose adenovirus vector, prompting widespread safety reforms in gene therapy.

Innocence Project

A non-profit legal organization founded in 1992 that uses post-conviction STR DNA fingerprinting and molecular evidence to exonerate wrongfully convicted individuals (including Malcolm Bryant in 2016).