Bio 251 Spring 2025 Final Exam Study Guide Flashcards

Flashcards covering key vocabulary and concepts from a Bio 251 lecture, Spring 2025.

Loss of Function Mutation

A protein is either non-functional or has reduced function; often recessive. Example: cystic fibrosis.

Gain of Function Mutation

New or enhanced activity of the protein, or activity in an inappropriate time or tissue; typically dominant.

Neutral Mutation

Change the amino acid sequence but do not significantly alter protein function.

Missense Mutation

Change one amino acid in the protein, which may or may not affect function, depending on the role of the amino acid.

Nonsense Mutation

Introduce a premature stop codon, usually making the protein non-functional.

Frameshift Mutation

Caused by insertions or deletions not in multiples of 3, shifting the reading frame.

Silent Mutation

Do not change the amino acid sequence due to codon redundancy, but can still affect gene expression, protein folding, or splicing.

Monohybrid Cross

One trait with two alleles. Example: Crossing RR with rr.

Segregation

Each individual has two alleles that separate during gamete formation.

Dihybrid Cross

Two traits, two genes with two alleles. Example: RRYY x rryy. Alleles at different loci segregate independently during gamete formation.

Complete Dominance

The heterozygote phenotype is identical to one of the homozygotes. Ex: RR and Rr both show the same phenotype; one allele completely masks the effect of the other.

Incomplete Dominance

The heterozygote has a phenotype intermediate between two homozygotes. Ex: RR (red) x rr (white) creates Rr (pink); neither allele is fully dominant, the heterozygote shows a blend.

Codominance

The heterozygote simultaneously expresses traits from both homozygotes. Ex: a white cow with brown spots. Both alleles are fully expressed, not blended.

Multiple Alleles

Refers to more than two alleles that exist in a single gene locus within a population. Each individual organism inherits two alleles, but more than two possible alleles can exist in the population. Ex. blood group in humans.

Epistasis

Occurs when the effect of one gene is masked or modified by one or more genes at different loci. The masking gene is called epistatic, and the gene being masked is hypostatic.

Inducible Operons

Genes are off by default, turned on by an inducer. Example: lac operon.

Repressible Operons

Genes are on by default, turned off by a corepressor. Example: trp operon.

Negative Control (Prokaryotes)

Repressor binds to operator to block transcription.

Positive Control (Prokaryotes)

Activator enhances RNA polymerase binding.

Attenuation

Early termination of transcription based on secondary mRNA structures.

DNA Replication

Occurs during the S phase of the cell cycle before cell division.

Mitosis

Produces two genetically identical daughter cells; chromosome duplicates and segregates equally; used for growth, tissue repair, and asexual reproduction.

Meiosis

Produces 4 non-identical haploid cells (gametes); includes two divisions: Meiosis I (homologous chromosomes separate) and Meiosis II (sister chromatids separate). Introduces genetic variation through crossing over (prophase I) and independent assortment (metaphase I).

Prophase (Mitosis)

Chromosomes condense and become visible, mitotic spindles begin to form from centrosomes, nucleus disappears.

Prometaphase

Nuclear envelope breaks down, spindle microtubules attach to kinetochore on centromeres.

Metaphase (Mitosis)

Chromosomes align along the metaphase plate; each chromosome is attached to spindle fibers from opposite poles.

Anaphase (Mitosis)

Sister chromatids separate and move toward opposite poles; each chromatid is now an individual daughter chromosome.

Telophase (Mitosis)

Chromosomes decondensed, the nuclear envelope reforms around each set of chromosomes, the spindle disassembles.

Cytokinesis

Cytoplasm divides, forming two separate daughter cells.

Prophase I (Meiosis)

Most complex phase; synapsis and crossing over between homologous chromosomes; chromosomes begin to condense, homologous chromosomes pair, crossing over, chromosomes fully condensed and ready for alignment.

Metaphase I (Meiosis)

Homologous chromosome pairs line up at the metaphase plate, and each pair attaches to spindle fibers from opposite poles.

Anaphase I (Meiosis)

Homologous chromosomes separate (sister chromatids stay together).

Telophase I and Cytokinesis

Nuclear membranes may reform, the cell divides into two haploid cells.

Prophase II (Meiosis)

New spindle apparatus forms, chromosomes condense again (still with 2 sister chromatids).

Metaphase II (Meiosis)

Chromosomes align at the metaphase plate.

Anaphase II (Meiosis)

Sister chromatids separate and move to opposite poles.

Telophase II and Cytokinesis

Nuclear envelope reforms, cytoplasm divides → 4 genetically distinct haploid cells.

Restriction Enzymes

Bacterial enzymes that cut DNA at specific sequences; serve as a defense system in bacteria by destroying invading viral DNA.

Recognition Site Binding

Each restriction enzyme recognizes a specific DNA sequence, typically 4-8 bp long and palindromic.

DNA Cleavage

The enzyme cuts both DNA strands at or near the recognition site, creating either sticky ends (overhanging single-stranded ends) or blunt ends (straight cuts across both strands).

Resulting Fragments (Restriction Enzymes)

The cut DNA can be joined with other DNA fragments having compatible ends using DNA ligase.

Restriction Endonucleases

Cut DNA within a specific sequence; internal cleavage at recognition sites; generates defined DNA fragments for cloning or analysis.

Exonucleases

Remove nucleotides one at a time from the end of a DNA strand; progressive digestion from 5’ or 3’ end; useful in deleting specific DNA regions, generating single-stranded templates, or preparing blunt ends.

CRISPR-Cas System

A genome editing tool derived from bacterial immune defense mechanisms allows for precise targeted changes to DNA in living cells.

How CRISPR Works

Design a gRNA that matches the DNA sequence, Cas9 binds the gRNA and scans DNA for the target sequence next to PAM site, Cas9 cuts both DNA strands at the target site, cell repairs the break using nonhomologous end joining or homology-directed repair.

Cas9 nickase

Cuts only one DNA strand, reduces off-target effects

dCas9 (dead)

Mutated Cas9 that binds DNA without cutting used for gene regulation.

Base Editors

Fuse Cas9 with enzymes to convert C→T or A→G without cutting DNA.

Prime Editing

Search and replace using Cas9 and reverse transcriptase

Cas12 and Cas13 Systems

Other enzymes that target DNA (CAS12) or RNA (CAS13) for broader uses.

Target specificity CRISPR

crispr uses a guide RNA that can be precisely programmed to target virtually any DNA sequence

Efficiency CRISPR

high success rate in introducing targets edits compared to older methods

Simplicity CRISPR

Easer to design and use- requires only cas protein and a gRNA

Versatility CRISPR

works in a wide range of organisms and cell types (bactria to mammals)

Multiplexing ability CRISPR

can edit multiple genes at once by introducing multiple gRNAs

Broad applications CRISPR

used for gene knockouts, insertions, base editing, epigenetic regulation, diagnosis, and mroe

Cost effective CRISPR

cheaper than older genome-editing technologies

Off-target effects CRISPR

cas enzymes may cut DNA at sites that are similar, but not identical, to the target, causing unwanted mutations

PAM sequence dependcent CRISPR

editing is restricted to DNA sequences near a PAM site

Delivery challenges CRISPR

delivering CRISPR components into some cell types can be difficult

Immunogenicity CRISPR

cas proteins can trigger immune responses in humans

Repair pathway limitations CRISPR

relies on cellular DNA repair mechanisms; nonhomologous end joining is error prone, whike homology-directed repair is less efficient

Mosaicism CRISPR

in multicellular organisms (like embryos), not all cells may be edited, leading to inconsistent outcomes

Ethical concerns CRISPR

can create heritable genetic changes with long-term consequences.

Gel Electrophoresis

DNA fragments are loaded into wells of a gel matrix (agarose), then an electric current is applied. Smaller fragments migrate faster and farther than larger ones, separating by size.

Capillary Electrophoresis

Used in automated DNA sequencing; DNA fragments migrate through a thin capillary filled with a gel-like polymer. A fluorescent dye attached to DNA enables laser detection at high resolution.

Southern Blotting

After gel electrophoresis, DNA is transferred to a membrane and hybridized with a labeled probe; allows detection of specific DNA sequences.

PCR Requirements

Template DNA, primers, DNA polymerase, dNTPs (A,T,C,G), buffer solution, thermal cycler.

PCR Steps

1. Denaturation (94-96 C): Heat the reaction to separate double stranded DNA into single strands. 2. Annealing (50-65 C): Cool the reaction to allow primers to bind to complementary sequences on the single stranded DNA. 3. Extension (72 C): DNA polymerase adds nucleotides to the 3’ ends of the primers to synthesize new DNA strands.

Gene Cloning

Producing identical copies of a specific DNA fragment by inserting it into a host organism—usually bacteria—where it can be replicated.

Isolate and Cut the DNA Cloning process

The gene of interest and plasmid vector are cut with the same restriction enzymes, creating compatible sticky ends.

Ligation Cloning process

The gene and vector are mixed and joined using DNA ligase, forming recombinant DNA.

Transformation Cloning process

The recombinant DNA is introduced into competent bacterial cells via heat shock or electroporation.

Selection Cloning process

bacteria are grown on selective media to identify those that took up the plasmid.

Replication and expression Cloning process

Inside the host, the plasmid is replicated, producing many copies. The gene may also be transcribed and translated into protein.

Sanger Sequencing (Dideoxy or chain termination method)

Uses DNA polymerase, a primer, template DNA, and a mix of normal nucleotides (dNTPs) and modified nucleotides (ddNTPs) that lack a 3’-OH group. When a ddNTP is incorporated, chain elongation stops because no further nucleotides can be added.

Next Generation Sequencing (NGS)

High throughput sequencing, sequences millions of DNA fragments in parallel, DNA is fragmented and attached to adapters, then immobilized on a solid surface, amplified into clusters and sequenced base-by-base using fluorescently labeled nucleotides, a camera captures real-time base addition at each cluster location.

Analyzing Short Tandem Repeats (STRs)

Short DNA sequences, 2-6 bp long, that are repeated in tandem at specific loci in the genome. The number of repeats vary among individuals, making STR regions highly polymorphic. Differences in repeat number form basis of a person's genetic fingerprint.

Forward Genetics Starting Point

Observed phenotype to identify the gene responsible for a trait; uses random mutagenesis.

Reverse genetics Starting Point

Known gene/DNA sequence goal to determine the function of a specific gene. Disrupts or modifies the gene and observes the resulting phenotype.

Targeted Mutagenesis

Introduce specific, intentional changes in the DNA sequence of a gene to study its function; alters known DNA sequences in precise locations.

Site Directed Mutagenesis

Introduces nucleotide changes at a defined site in a DNA molecule; change a single amino acid to study protein function; test effects of regulatory element changes.

Gene Knock-in

A modified or foreign gene is inserted into a specific locus in the genome

Forward Genetics Key Methods

Start with an observable trait and work backwards to identify the gene responsible

Reverse Genetics Techniques

Start with a known gene and disrupt or modify it to see what effect it has on the organism

Gene Knock-out reverse genetics

Entire gene is deleted or inactivated, observes what function is lost

Homology Analysis

Compares the gene to similar genes in other species. If a gene is conserved, it likely has an essential function.

Gene Ontology and Databases Biotechnologu

Binds to DNA, use annotations from genome databases to predict function based on known genes

Production of therapeutic proteins Biotechnology

Replaces animal-derived insulin, Growth Hormones, clotting factors, and vaccines

Gene Therapy Biotechnology

Faulty or missing genes are replaced or corrected in a patient's cells; used in treatment of genetic disorders.

CRISPR based therapies Biotechnology

Precisely edits genes in human cells, trials underway for sickle cell disease and some cancers.

Personalized medicine Biotechnology

Genetic profiling helps tailor drug treatments to individuals.

Disease diagnosis Biotechnology

PCR and molecular probes detect infection quickly and accurately; genetic testing identifies carriers or hereditary diseases.

Genetically modified crops Biotechnology

Crops are engineered for: insect resistance, herbicide tolerance, drought or salt tolerance, nutritional enhancement.

Improved animal breeding Biotechnology

Animals are engineered for: higher milk production, leaner meat, disease resistance

Gene editing in plants and animals Biotechnology

CRISPR used to develop: disease-resistant pigs, non-browning mushrooms, allergen-free wheat.

Biofactories

Plants and animals engineered to produce pharmaceuticals or industrial enzymes.

Restriction Enzymes terminology

Proteins that cut DNA at specific nucleotide sequences. Can cut in two ways: blunt and sticky ends.

Restriction Sites Definition

Each enzyme recognizes a specific sequence of bases (usually 4-8 bp) called a recognition site - Usually a short, palindromic DNA sequence (4-8 bp long)

Sticky Ends

Single stranded overhangs of DNA that result when a restriction enzyme cuts DNA in a staggered fashion Can easily base-pair with complementary sequences