Biology 142 MasterDoc

skin, mucus, stomach acid

First line of innate immunity

Phagocytosis

Process where cells like macrophages engulf and digest pathogens

Macrophage role

Engulfs pathogens and presents antigens to T cells

Neutrophil role

Fast-acting phagocyte that attacks bacteria

Dendritic cell role

Professional antigen-presenting cell that activates T cells

Inflammation purpose

Brings immune cells and resources to the infection site

Fever purpose

slows pathogen growth and boots immune

Adaptive immunity key feature

Learns and remembers specific pathogens

Antigen definition

A molecule that triggers an immune response

Epitope

The specific part of antigen an antibody binds

Clonal selection

Only B or T cells that recognize the antigen multiply

Plasma cell

A B cell that produces large amounts of antibodies

Memory B cell

Long lived B cell that responds quickly on re-exposure

Memory T cell

Long lived T cell that activates rapidly on re-exposure

Helper T cell activation requirement

Must see antigen presented on APC

Cytotoxic T cell activation requirement

Must recognize antigen infected cells

Antibody neutralization

Antibodies block pathogens

Opsonization

Antibodies tag pathogens for phagocytes to eat

Complement activation

antibodies trigger proteins that destroy microbes

Humoral immunity target

pathogens in body fluids (extracellular)

Cellular immunity target

infected or abnormal cells (intracellular pathogens)

APC examples

macrophages, dendritic cells, B cells

Why adaptive immunity is slow at first

B and T cells must be activated and multiply

Why adaptive immunity is fast later

memory cells respond immediately

Vaccine Purpose

create memory cells without causing disease

antibody class IgM

first antibody made during primary response

antibody class IgG

main antibody in secondary response

Where B cells mature

Bone Marrow

Where T cells mature

Thymus

What activates B cells

Binding antigen and receiving help from helper T cells

What is CRISPR originally in nature?

A bacterial immune system that stores viral DNA “memories” and uses them to defend against future infections.

What does Cas9 do in the natural CRISPR system?

It acts as a DNA-cutting enzyme (“molecular scissors”) that destroys viral DNA.

What is a CRISPR spacer?

A short piece of viral DNA inserted into the bacterial genome as a memory of past infection.

What are the three stages of CRISPR immunity?

Adaptation (store viral DNA), Expression (make guide RNAs), Interference (Cas9 cuts matching viral DNA).

How do restriction enzymes protect bacteria?

They cut foreign (unmethylated) viral DNA at specific sequences, destroying it.

Why don’t restriction enzymes cut bacterial DNA?

Bacterial DNA is methylated, which protects it from being cut.

How is CRISPR immunity different from restriction enzyme immunity?

CRISPR is adaptive (stores memories of specific viruses); restriction enzymes are innate (cut any unprotected DNA).

What is the role of crRNA in CRISPR?

It contains the viral memory sequence and guides Cas9 to matching viral DNA.

What is the role of tracrRNA?

It helps Cas9 function and pairs with crRNA to form the guide complex.

What happens when viral DNA matches the crRNA sequence?

Cas9 is guided to the viral DNA and cuts it, stopping infection.

What is CRISPR‑Cas9 technology?

A lab‑engineered system that uses Cas9 and a guide RNA to cut DNA at a chosen location in eukaryotic cells.

How is the guide RNA (sgRNA) different from natural CRISPR RNAs?

sgRNA combines crRNA + tracrRNA into one molecule to simplify targeting.

What does the sgRNA do in CRISPR editing?

It directs Cas9 to a specific DNA sequence by base‑pairing with the target.

What is the PAM sequence and why is it required?

A short DNA motif (usually NGG) next to the target site; Cas9 can only bind and cut if PAM is present.

What happens when Cas9 cuts DNA in a eukaryotic cell?

The cell activates DNA repair pathways, which create the genetic edit.

What is donor DNA used for in CRISPR editing?

It serves as a template for precise repair during HDR, allowing insertion or correction of sequences.

What is the difference between endogenous CRISPR and CRISPR technology?

Endogenous CRISPR protects bacteria from viruses; CRISPR technology is engineered for genome editing in other organisms.

What is NHEJ (Non‑Homologous End Joining)?

A fast, error‑prone DNA repair pathway that joins broken ends and often creates insertions/deletions.

What is HDR (Homology‑Directed Repair)?

A precise repair pathway that uses a donor DNA template to fix or replace sequences.

Which repair pathway is more accurate: NHEJ or HDR?

HDR is more accurate because it uses a template; NHEJ is sloppy and introduces random mutations.

What type of edit does NHEJ usually create?

Small insertions or deletions (indels) that often disrupt or knock out a gene.

What type of edit does HDR allow?

Precise edits such as gene correction, gene replacement, or insertion of new DNA.

When is NHEJ preferred in CRISPR editing?

When the goal is to knock out a gene or stop a protein from being produced.

When is HDR preferred in CRISPR editing?

When the goal is to fix a mutation, add a gene, or make an exact sequence change.

Why is HDR less efficient than NHEJ?

HDR only occurs during certain cell cycle phases (S/G2) and requires donor DNA, making it slower and less common.

What limits where Cas9 can cut in the genome?

The need for a PAM sequence (e.g., NGG) next to the target site.

What is an off‑target effect in CRISPR editing?

When Cas9 cuts at a similar but unintended DNA sequence, causing unwanted mutations.

How do scientists reduce off‑target effects?

By designing highly specific sgRNAs, using high‑fidelity Cas9 variants, and checking for similar sequences in the genome.

Why does CRISPR work in eukaryotic cells even though it evolved in bacteria?

Because Cas9 only needs DNA, a guide RNA, and a PAM — all of which exist in eukaryotic cells.

What are the essential components needed for CRISPR editing in a eukaryotic cell?

Cas9 enzyme, sgRNA, target DNA sequence, PAM, and (for HDR) donor DNA.

What is Mendel’s Principle of Segregation?

Each gamete receives only one allele of a gene because homologous chromosomes separate during Anaphase I of meiosis.

What is Mendel’s Principle of Independent Assortment?

Alleles of different genes assort independently because homologous chromosome pairs align randomly at Metaphase I.

What meiotic event explains segregation?

Anaphase I — homologous chromosomes (with different alleles) separate.

What meiotic event explains independent assortment?

Random orientation of homologous chromosome pairs at Metaphase I.

How does independent assortment generate variation?

Each chromosome pair aligns independently → produces 2ⁿ possible gamete combinations.

What is the genotype → phenotype relationship?

Genes encode proteins, and protein function produces the trait.

Pea shape example: What does the R allele do?

R allele makes a functional enzyme that converts sugars → starch → round peas.

What does the r allele do?

r allele is loss‑of‑function → no enzyme → excess sugar → uneven drying → wrinkled peas.

Why is R dominant over r?

One working R allele makes enough enzyme → round phenotype → gene is haplosufficient.

What makes an allele dominant?

It produces enough functional protein to determine the phenotype in heterozygotes.

What makes an allele recessive?

It is usually loss‑of‑function and only shows phenotype when both alleles are mutant.

What is a loss‑of‑function allele?

Mutation that reduces or eliminates protein activity; often recessive.What is a gain‑of‑function allele?

What is a gain‑of‑function allele?

Mutation that creates new, increased, or misregulated protein activity; often dominant.

How do you recognize a gain‑of‑function allele?

Heterozygote shows a new or overactive phenotype not seen in wild‑type.

What is haplosufficiency?

One functional allele is enough for normal phenotype → heterozygote looks normal.

What is haploinsufficiency?

One functional allele is not enough → heterozygote shows mutant phenotype.

What is a testcross?

Cross an individual with dominant phenotype (A?) to aa to determine if it is AA or Aa.

How do you interpret a testcross?

• 1:1 ratio → Aa

• All dominant → AA

What is a monohybrid cross?

Aa × Aa → genotype 1:2:1, phenotype 3:1 (if simple dominance).

What is a dihybrid cross?

AaBb × AaBb → phenotype 9:3:3:1 if genes assort independently.

What does a 9:3:3:1 ratio indicate?

Two genes, independent assortment, simple dominance at both loci.

What does a 1:2:1 phenotype ratio indicate?

Incomplete dominance or codominance — heterozygote has distinct phenotype.

What is epistasis?

One gene masks or modifies the phenotype of another gene.

What ratio indicates recessive epistasis?

9:3:4 phenotype ratio.

What ratio indicates dominant epistasis?

12:3:1 phenotype ratio.

What is a complementation test?

Cross two mutants with the same phenotype to determine if mutations are in the same gene or different genes.

How do you interpret a complementation test?

• Wild‑type offspring → different genes (complement)

• Mutant offspring → same gene (fail to complement)

How do you identify a haploinsufficient gene from a cross?

Heterozygote shows mutant phenotype → one copy isn’t enough.

How do you identify a haplosufficient gene from a cross?

Heterozygote shows normal phenotype → one copy is enough.

How do you tell LOF vs GOF from crosses?

• LOF: Homozygous mutant shows phenotype; heterozygote normal (haplosufficient) or mutant (haploinsufficient).

• GOF: Heterozygote shows new/overactive phenotype.\