Genetics & Molecular Biology Midterm

Open Reading Frame (ORF)

A stretch of nucleotides that, read as triplets from a starting point, is uninterrupted by a stop codon. Long ORFs suggest a protein-coding gene because random DNA would hit a stop codon roughly every 21 codons (3 of 64 triplets are stop codons).

Single Nucleotide Polymorphism (SNP)

A single base-pair difference between individuals; occurs about once per 1000 bp in the human genome. Most are in non-coding regions and silent, but some change protein sequence and can correlate with disease risk or drug response (pharmacogenomics).

DIP / InDEL

An insertion or deletion polymorphism, 1–100 bp long, occurring roughly once per 10 kb.

Simple Sequence Repeat (SSR)

A short repeated motif (1–10 bp unit), occurring about once per 30 kb; the NUMBER of repeats varies between people/chromosomes, which is the basis of DNA fingerprinting.

Copy Number Variant (CNV)

Larger tandem repeats (10 bp – 1 Mb); usually arise from unequal crossing-over/misalignment in meiosis and are typically inherited rather than new mutations.

Sanger Sequencing

Chain-termination sequencing using fluorescently labeled nucleotides; highly accurate, reads about 600–700 bp; the classic method for confirming a specific sequence (e.g., one SNP site).

Next-Generation Sequencing (NGS)

High-throughput, simultaneous sequencing of millions of random DNA fragments; overlapping reads are computationally assembled into longer sequences.

CODIS

The FBI's DNA database that stores SSR genotypes (13+ loci) used to match crime-scene DNA to individuals or exclude suspects.

Enhancer

A DNA sequence, often far from the gene (5' or 3'), that increases or represses basal transcription; still works when moved to a different position/orientation relative to the promoter.

Transcription Factor

A sequence-specific DNA-binding protein that binds promoters/enhancers and recruits other proteins to influence transcription. ~2000 exist in the human genome; types include basal factors, activators, and repressors.

TATA box

A eukaryotic core promoter element located ~25–30 bp upstream of the transcription start site, essential for initiation; unlike bacteria, each eukaryotic gene has its own promoter (mRNAs are NOT polycistronic).

Chromatin Remodeling Complex

A protein complex that unwinds/repositions DNA around nucleosomes so that promoter/enhancer sequences become accessible for transcription factor binding.

Histone Acetylation

Addition of acetyl groups to histone tails; loosens nucleosome packing → favors euchromatin/active transcription (reversed by histone deacetylases).

Histone Methylation

Addition of methyl groups to histone tails; effect depends on the residue — e.g., methylation of H3K9 favors heterochromatin/silencing (reversed by histone demethylases).

RNA Processing

5' capping, 3' polyadenylation, and splicing (removal of introns, joining of exons) that convert a primary transcript into mature mRNA.

Alternative Splicing

Different combinations of exons are joined in different cells/tissues/stages, producing multiple protein isoforms from one gene; affects ~95% of human multi-exon genes.

MicroRNA (miMRNA)

A small regulatory RNA processed from a primary transcript (Drosha cuts pri-miRNA → pre-miRNA; Dicer cuts pre-miRNA → mature duplex). One strand loads into RISC to regulate mRNA.

RNA Interference (RNAi)

Experimental technique using synthetic double-stranded RNA processed like miRNA and loaded into RISC; perfect complementarity to a target mRNA leads to its degradation, knocking down gene expression.

RNA Induced Silencing Complex (RISC)

The complex carrying a mature miRNA/siRNA strand; perfect complementarity to target mRNA → mRNA degraded; imperfect complementarity → translation repressed.

Fertility Factor (F)

A conjugative plasmid (~100 kb, 1–2 copies/cell) that confers donor status. F+ cells (have F) donate to F– cells (lack F) via a pilus.

Conjugation

Cell-to-cell DNA transfer through a pilus. F is replicated by the rolling-circle mechanism; a single strand transfers to the recipient, where the second strand is synthesized and ligated into a circle, converting the recipient to F+.

Episome

A plasmid (like F) capable of integrating into the host chromosome via recombination between IS elements shared by both.

High Frequency Recombination Cell (Hfr)

A cell in which F has integrated into the bacterial chromosome; different Hfr strains have F integrated at different locations/orientations, transferring chromosomal genes in different orders during conjugation.

Transformation

Bacteria take up naked DNA from the environment; one strand binds the recipient's receptor site, integrates, and recombines into the homologous region of the chromosome (the other strand is degraded).

Cotransformation

Two genes transferred together at a frequency higher than the product of their individual transformation frequencies, implying they lie close together — used to map gene order.

Transduction

Bacterial DNA transferred from one cell to another by a bacteriophage. Generalized transduction can move DNA from anywhere in the chromosome; specialized transduction moves genes from one particular region.

Cotransduction

Two genes packaged and transferred together in the same phage particle; frequency increases the closer together the genes are — used for fine-scale linkage mapping.

Operon

A unit of DNA with structural genes (usually several, transcribed as one polycistronic mRNA) plus a promoter and an operator, all regulated together.

Polycistronic mRNA

A single mRNA encoding several proteins, each with its own ribosome-binding site and start codon; common for genes in the same pathway.

Promoter

The RNA polymerase binding site; in bacteria, sigma factor increases RNA polymerase's affinity for the promoter during initiation.

Operator

A DNA sequence (usually overlapping/near the promoter) that a repressor protein binds to block transcription.

Repressor

A protein whose binding to the operator blocks transcription; must be REMOVED for transcription to proceed.

Negative Regulation

Default state is ON in a system controlled purely by a repressor, unless the repressor is normally bound

Inducer

A small molecule (e.g., allolactose, a lactose derivative) that binds a repressor and changes its shape so it can no longer bind the operator → turns transcription ON.

Positive Regulation

Default state is OFF until an activator protein binds and helps recruit RNA polymerase (e.g., CRP on the lac promoter).

Corepressor

A small molecule (e.g., tryptophan) that binds an inactive aporepressor, activating it so it CAN bind the operator → turns transcription OFF (used in repressible systems like trp).

Catabolite Repression / CRP-cAMP System

When glucose is abundant, cAMP is low, so CRP cannot activate the lac promoter efficiently — lac operon stays low even if lactose is present. When glucose is scarce, cAMP rises, binds CRP, and CRP boosts RNA polymerase's affinity for the lac promoter.

Genotype

The genetic makeup (alleles) that an organism carries.

Phenotype

The physical observable trait produced by genotypes.

Allele

An alternative form of a gene (e.g., yellow vs. green seed color alleles).

Dominant / Recessive

The dominant allele determines the phenotype in heterozygotes; the recessive allele's effect only appears in homozygotes.

True-Breeding

A self-fertilized strain that always produces offspring identical to itself for a given trait.

Monohybrid Cross

A cross between two individuals heterozygous for ONE gene (Aa × Aa); F2 ratio = 3 dominant : 1 recessive.

Dihybrid Cross

A cross tracking TWO genes at once (e.g., AaBb × AaBb); F2 ratio = 9:3:3:1.

Testcross

Crossing an individual of unknown genotype (but dominant phenotype) with a homozygous recessive individual, to reveal whether the unknown is homozygous (all offspring look alike) or heterozygous (1:1 ratio of phenotypes).

Law of Independent Assortment

Alleles of different genes segregate independently of one another during gamete formation (true as long as genes are on different chromosomes or far apart on the same one).

Law of Dominance and Uniformity

An organism with at least one dominant allele shows the dominant phenotype; all F1 heterozygotes from a true-breeding cross look uniform.

Sum Rule

The probability of EITHER of two mutually exclusive events = the sum of their individual probabilities (used for 'or' — e.g., probability of being WW or Ww).

Product Rule

The probability of two INDEPENDENT events both happening = the product of their individual probabilities (used for 'and' — e.g., probability of being round AND green).

Carrier

A heterozygous individual who does not show a recessive phenotype but can pass the recessive allele to offspring.

Hemizygous

Having only one copy of a gene — describes males for X-linked genes (only one X chromosome).