final exam Flashcards

Question

Complementation test

Answer 1

used to determine whether 2 mutations that produce the **same phenotype are in the same gene or in different genes** *"are the different dumpy strains mutated in the same gene or different genes?"* - if 2 mutations are in **different genes** = the 2 non-mutated copies (one from each parent) can "complement" each other to **restore the normal phenotype** - if on **same gene** → no normal copy to compensate → **mutant phenotype remains**

Answer 2

corn snake skin color is determined by 2 genes: **R locus**: orange pigment enzyme (R allele makes enzymes) **B locus**: black pigment enzyme (B allele makes enzymes) "In some cases, multiple genes act **independently**, and the observed **phenotype is the sum of the products**, similar to incomplete dominance at a single locus both R & B = orange + black = red both r and b = no orange and no black = albino same with black and orange

Answer 3

in some cases, multiple genes contribute to a single trait, acting **independently and additively** - phenotype depends on sum of effects of individual genes, similar to incomplete dominance - ex. corn snake skin color *different from epistasis which is when one worker paints over the work of another worker while additive effect is they both work together to contribute to wall without interference*

Answer 4

one gene **masks or modifies** the effects of another gene on particular phenotype - often because genes are in the **same pathway** **example**: coat color in Labrador retrievers - B locus (determines pigment black or brown) = make black pigment from brown pigment - E locus (determines pigment deposition, color visible or yellow coat) = make brown pigment from yellow pigment - when epistasis occurs, observed phenotypic ratios in offspring will **deviate from expected mendelian ratios (F2 = 9:4:3)**

Answer 5

**IF** the genes R and B in corn snake skin act *independently and additively* - but this assumes no interaction between the genes - but in additive inheritance, there is still some interaction because the effects are cumulative so the relationship is more complex (ex. 1:4:6:4:1)

Answer 6

*additive effects of multiple genes can also be used to model continuous traits* - in these cases, phenotype is determined by the combined effects of many genes, each with a small effect **example**: trait controlled by 3 genes, each w 2 alleles (one for brown and one for white). individuals with more brown have darker phenotype and more white have lighter phenotype - result of continuous distribution of phenotypes from very dark to very light

Answer 7

**TYRP1 (B Locus)**: encodes enzyme involved in production of brown pigment - *B allele* codes functional enzyme (black pigment), while *b allele* is non-functional (brown pigment) **MCR1R (E Locus)**: encodes receptor protein that plays crucial role in determining whether any pigment (black or brown) is produced at all - *E allele* codes functional receptor (allowing pigment production), while *e allele* codes non-functional receptor (blocks pigment synthesis regardless of genotype at B locus) therefore, **e allele of MCR1R is epistatic to alleles at TYRP1 (B) locus** so 2 copies of e allele (ee genotype) = no pigment so yellow color irrespective of whether B or b (labrador retrievers)

Answer 8

mutation in another gene that **reduces the effect** of the first mutation - often encode proteins that interact with the protein encoded by the first gene - ex. gene m mutation so proper complex cannot be formed but mutation in s compensates, permitting complex formation - but mutation in *s* *without mutation* in *m* cannot form active complex **suppressors in same pathway**: reduce effect of original mutation by acting in the same pathway - ex. gain of function mutation in suppressor gene can compensate for loss-of-function mutation in original gene, restoring normal phenotype **suppressors in parallel pathways**: can also occur in genes that function in parallel pathways - ex. mutation in gene A leads to mutant phenotype, suppressor mutation in gene B in parallel pathway can compensate and restore normal phenotype *opposite manner of synthetic mutations*

Answer 9

**identifying genes in pathways**: mutagenize organisms w/ mutations of interest and screen for suppressor mutations that restore the wild-type phenotype → identify genes w/ suppressor mutations that reveal other genes involved in the same pathway **drug target identification**: suppressor screens are powerful ways to identify drug targets for genetic disease - inhibit drug in parallel pathway → possible to suppress effects of a disease-causing mutation **understanding human disease**: individuals found that have strong mendelian genetic disease but they're very healthy due to unknown suppressor alleles - investigation into these suppressor alleles could lead to novel therapeutic strategies for treating these diseases

Answer 10

2 mutations, which individually cause no or minor defects, together produce a **severe phenotype** - mutant phenotype observed **only when both genes are mutated** - act in manner opposite to the suppressor mutations

Answer 11

Drosophila suppressor and synthetic alleles were used to map signaling pathways used by growth factors and the Ras oncogene (mutated causes cancer) to regulate cell division C. elegans - both were used to study apoptosis these pathways are conserved in humans so understanding them provides insight into diseases like cancer

Answer 12

even with identical genomes, individuals can exhibit range of phenotypes due to factors like penetrance, expressivity, conditional alleles, and genetic buffering

Answer 13

these traits are determined by the combined effects of multiple genes, each with a small effect

Answer 14

**sex differences**: same genotypes for most genes, but different phenotypes - ex. voice pitch, behaviors, and other secondary sexual characteristics are heavily sex-influenced - variable penetrance - variable expressivity - environmental effects - conditional alleles - developmental noise - somatic events: things like X activation - transcription/translation variability: randomness in gene expression - gene expression differences in heterozygotes: cells might express more of one allele than the other

Answer 15

**osteogenesis imperfecta**: autosomal dominant disorder, is 100% penetrant (everyone with the mutation exhibits some phenotype), but the severity of the phenotype can vary greatly. - ranges from blue eyes to severe skeletal abnormalities or anything in between **BRCA 1** - heterozygote mutant women have 50% higher risk of breast cancer **neurodibromatosis**: autosomal dominant disorder, exhibits incomplete penetrance (50-80%), meaning not everyone with the mutation develops symptoms - but even among those who have it **variable expressivity** - ranges from skin splotches to massive tumors

Answer 16

**variable penetrance**: not everyone with a particular genotype shows the associated phenotype (some individuals have the trait, others do not) - ex. BRCA 1- heterozygote women have 50% higher risk of breast cancer, osteogenesis imperfecta, neurofibromatosis **variable expressivity**: the extent to which a phenotype is expressed varies among people (all individuals have trait, but different amounts of it) - ex. *deleting exon 6 from mice TBXT results in heterozygote short/no tail mice* (all have short tails but some have shorter tails than others)

Answer 17

genetical identical individuals in different environments have different phenotypes - ex. risk of breast cancer alters by lifestyle - *himalayan rabbits* have temp sensitive alleles of melanin producing enzyme (if temp less than 25ºC, extremities turn black while rest of rabbit is white)

Answer 18

**conditional alleles**: alleles whose phenotype depends on environment - **auxotroph mutations** are conditional alleles: genetic mutation that causes an organism to lose ability to produce vital nutrient for growth (in bacteria prevent growth in minimal media unless required nutrient is supplied) ex. **phenylketonuria (PKU)**: leads to brain damage but can be avoided is homozygous recessive individuals avoid eating phenylalanine ex. **(ts) alleles in Drosopholia**- ts means temp sensitive, neurotransmission at high temperatures but no effect at lower temps - temp sensitivity makes them useful tools for studying the nervous system

Answer 19

**developmental noise**: random fluctuations during development can affect phenotype examples: inverted sides of face, identical twins with different fingerprints **waddington's landscape**: metaphor for development and phenotypic variability - ball starts same but hills and valleys so rolling down ends up at different endpoint - **THE HILLS AND VALLEYS**: explains things like mosaics (like McClintock's maize), transcriptional/translational variability

Answer 20

**X-inactivation**: process in female mammals where 1 of 2 X chromosome in each cell is randomly inactivated during embryonic development - ensures that only 1 X chromosome is active per cell, preventing overdose of X-linked gene products creates **Barr bodies** (the inactivated X copy) *example is calico coat color in cats, O allele is the inactivated one, so either orange or black fur expressed*

Answer 21

**genetic buffering**: ability of some genes to buffer ("mask") the effects of mutations in other genes → **reduces phenotypic variability** **hsp90**: highly conserved *molecular chaperone* that helps proteins fold correctly, stabilizes them, and assists in their proper functioning; some mutations lead to them misfiling and HSP90 rescues them, ensuring they still function properly - under stressful conditions (like heat shock) → hsp90 ability reduced → previously masked genetic mutations are exposed → phenotypic changes ex. FANFA (fanconi anemia - autosomal recessive anemia) protein interacts with hsp90 increasing severity of mild FANCA mutations

Answer 22

**GFP**: green fluorescent protein - used as marker to measure gene expression levels - cells with more GFP glow brighter **TetR repressor**: TetR is a protein that can bind to DNA and inhibit transcription of specific genes - **negative feedback loop**: when TetR levels are high, suppresses its production and when TetR levels are low → resumes production **feedback reduces phenotypic variability** because without feedback, the TetR gene (and GFP indirectly) is expressed freely and levels fluctuate randomly ("noise") - but when feedback is there, TetR levels are regulated, stabilizing GFP levels

Answer 23

**qualitative**: either-or (binary traits) like yellow or green **quantitative**: composed of multiple underlying distributions - ex. height, "intelligence," heart disease, hair loss, diabetes, personality traits

Answer 24

**GWAS**: used to **identify genes** or genetic variants associated with **specific traits or diseases** - involves genotyping thousands of people & comparing their genotype at different locations in the genome - useful for genes that are *variable* and have *small effects* **SNPs (single nucleotide polymorphisms)**: common genetic variations that can be used as markers (should use markers that don't have any effect on the gene itself and are put in b/w gene regions that do not bind transcription factors) - **microarrays & PCR** are techniques used to genotype SNPs - SNPs are crucial for GWAS = ex. if specific SNP is common in diabetes patients than those without, it might point to a gene related to diabetes risk

Answer 25

method for **finding genes** associated with a particular trait when the **gene's function is unknown** - relies on principle that genes located near each other on chromosome tend to be inherited together 1. identify DNA markers that are known (polymorphic sites) - like SNPs or Microsatellites 2. narrow down region to pinpoint approximate location of gene on chromosome by finding markers closely linked to the gene 3. fine tune using markers near that gene 4. candidate gene analysis *has to do with GWAS I think*

Answer 26

because they affect protein activity or levels, not whether the protein is made or not - hard to identify since individuals are more-or-less OK, but at increased or decreased risk of a disease when averaged over **large population**

Answer 27

QTL mapping and GWAS are related but not the same **QTL mapping**: - uses experimental crosses (breeding plants or animals) - requires controlled genetic background - explores large chromosomal regions and focuses on lineage **GWAS**: - uses natural population, like humans, without experimental crosses - explores SNPs across genome - focuses on detecting associations at a fine scale, often identifying much smaller regions

Answer 28

statistical method in GWAS to control for **false positives** *false positives*: associations that appear significant by chance - basically computer finds the optimal p-value based on the data that you have - **FDR is data-set dependent** different from **Bonferroni's Correction method** which basically lowers the threshold for significance but issue is that you miss true associations (*false negatives*

Answer 29

statistical measure used in GWAS to evaluate strength of evidence supporting association between SNP and trait - used in Bayesian GWAS to complement or replace traditional p-value thresholds (directly compares likelihood of data under 2 hypothesis of association and no association and provides measure of evidence for each) *whereas p value tests probability of observing data if theres no association*

Answer 30

**effect size**: "how important is this gene?" - with large populations, GWAS can detect genes that are statistically significant yet have tiny effect that might not even be biologically meaningful **effect sizes matter!!**

Answer 31

combines effects of multiple alleles to predict an individual's phenotype for a complex trait - once computational model is trained, can **predict phenotype** of new individuals based on their genotypes - not a very accurate prediction, but **on average** does well - reflect genetic predisposition but environmental factors play a big role (ex. height) R^2 value = 0.11 means 90% of variation due to factors not measured by GWAS (not genetic)

Answer 32

because in order to be widespread, needs to be small otherwise everyone dies and the mutation doesnt even exist down the line

Answer 33

mixing & matching pieces of DNA to create new combinations new DNA molecule might have new or improved traits - screen/select for improved variants using cheap high-throughput **assay**

Answer 34

method scientists use to speed up the natural process of evolution in the lab - like giving nature a little push to create something specific *involves creating variations, identifying better variants, repeating process to create highly optimized molecules* - farmers have been doing this for a long time without even knowing **example in the slides**: artificial Diels-Alderase - computer based enzyme that was 10000x better

Answer 35

process of **introducing foreign material (like DNA)** into mammalian cells, with goal of **cells taking up material** and using it to produce proteins or alter their genetic makeup - common step in gene therapy, where scientists try to fix or replace faulty genes **tools used**: - **lipid nanoparticles**: tiny fat-like bubbles that can carry genetic material (DNA or RNA) into cells -**viral vectors**: modified viruses used to deliver genes into cells; harmful parts of virus are removed - **microinjection**: directly injecting genetic material into single cell - **calcium phosphate (Ca3(PO4)2) mediation**: forms small particles with DNA that can stick to cell surface and be taken up by the cell

Answer 36

**CRISPR-associated protein 9** protein that cuts DNA and is used in genetic engineering and genome editing

Answer 37

blood cells derived from bone marrow

Answer 38

developed by David Liu **attaches a base deaminase enzyme to deactivated cas9** = way of precisely changing just 1 letter in the entire genome - successfully used to inactivate PCSK9 in monkey liver cells (PCSK9 loss of function allele causes lower LDL cholesterol *basically hijacking liver*) - seems to be successful in human trials but businesses don't wanna fund it because its too much of a quick fix = not a good business model

Answer 39

**dolly the cloned sheep**: used a sheep skin cell to genetically clone a sheep named Dolly - proved existence of egg/ES (**embryonic stem cells**) cell factors that can drive "de-differentiation" (reboot)

Answer 40

embryonic stem cells

Answer 41

**induced pluripotent** (can become an cell type in the body) cells - generated from differentiated cells by expressing specific transcription factors (*notably KLF4, SOX2, c-myc, Oct-3/4)

Answer 42

- scientific community restricted embryo research to the first 14 days and prohibiting implantation (embryo discarded after 14 days) **controversial case of Jiankui He**: edited CCR5 gene in human embryos to confer HIV resistance

Answer 43

way to check the genetic health of embryos before they are implanted into the uterus during **IVF (in vitro fertilization)** - embryo screening to test only the healthy embroys and implanting those

Answer 44

**cyclin proteins** - are there and then go away during some parts and come back - why they're called "cycle"

Answer 45

proteins that act like traffic controllers for the cell cycle need to partner up with **cyclins** to become active once active, CDKs add chemical tags to other proteins (**phosphorylate them**) to signal the cell to move to the next stage of the cell cycle different CDKs are active at different times to ensure cell cycle works in the right time and order

Answer 46

**G1 checkpoint**: monitors for DNA damage and sufficient cell size before allowing cell to progress to S phase (DNA replication) **G2 checkpoint**: checks for DNA damage and complete DNA replication before cell enters mitosis (M phase) **M checkpoint**: ensures that chromosomes are properly attached to the spindle fibers before proceeding to anaphase (sister chromatids are separated) - if any of these things are not done, then cell cycle is halted until the damage is fixed. if not fixed, then **apoptosis**

Answer 47

**1. positive regulation by cyclin protein levels** - when cyclin levels increase, CDKs pair with them & become active - ensures that *CDKs are only active when needed*, like during specific stages of the cell cycle **2. inhibitory phosphorylation of the kinase subunit** - even when CDKs are paired with cyclins, can be *temporarily turned off* by adding chemical tag called *phosphate group* - acts like a brake stopping the CDK from working until cell is ready

Answer 48

**telomere length**: cells stop dividing when the telomeres shrink (protective caps at the end of chromosomes) **anchorage dependence**: cells needs to be attached to a solid surface to divide **density-dependent inhibition**: cells stop dividing when they start to touch other cells *cancer cells hallucinate all of this and think its not happening*

Answer 49

**metastasis**: get out of membranes by making enzymes and chewing their way out (what makes a tumor malignant) **angiogenesis**: feed themselves by secreting growth factors to promote blood vessel development

Answer 50

**inhibit cell growth** - once they're mutated, cells can divide unconditionally = cancer - ex. **Rb protein** that blocks E2F transcription factor required to drive DNA synthesis - also **p53** ("defender of the genome") - **BRCA1** (also tumor suppressor, if it gets mutated then can get breast cancer)

Answer 51

**tumor suppressor**: *loss* of function mutations **oncogenes**: gain-of-function mutations - promote the cell cycle **proto-oncogenes**: also promote cell division, but normal version (not yet mutated) - can become oncogenes

Answer 52

**growth factor**: proteins released by certain cells that stimulate other cells to divide **growth factor receptors**: required for responding to growth factors **growth factor signaling molecules**: transmit signals from growth factor receptors to promote cell division (machinery inside cell that send message to nucleus from receptor) *activated inappropriately* = cancer (uncontrolled cell growth)

Answer 53

highlights observation that **larger animals w/ more cells do not get cancer more frequently** *explained by:* - increased apoptosis in elephant cells - multiple copies of p53 tumor suppressor gene in elephants

Answer 54

**Ras**: "molecular switch" in signal transduction pathway that sends signals to cells that growth factor is present - *single amino acid change* in Ras protein can cause stimulation of pathway, even in the *absence of growth factors* = cells hallucinate growth factor = become cancerous **abL**: kinase that mediates growth factor signals - *translocation outs abL under control of the bcr promoter* = over expression of gene = driving cell division and contributing to chronic myelogenous leukemia (CML) **bcL**: protein that prevents apoptosis - translocations can lead to bcL over expression = prevent cells from undergoing apoptosis when they should = B-cell lymphoma

Answer 55

**translocation**: gene moved to new locus, under new controls - *new fusion gene created that can drive uncontrolled cell growth* **point mutation within the gene**: random change in DNA sequence when a base pair is added, deleted, or substituted - *hyperactive or degredation-resistant protein* **gene amplification**: normal growth-stimulating protein in excess **point mutation in a control element**: normal growth-stimulating protein in excess

Answer 56

- explains how mutations in tumor suppressor proteins can lead to cancer **hets** (who inherit one copy of tumor suppressor gene) are more susceptible to cancer b/c they require only one additional mutation in remaining copy to lose tumor suppressor gene's function - the longer you live = the more cell divisions you have = greater chance of cancer **multi-hit model**: cancer development is a multi-step process, multiple mutations accumulated over periods of many years

Answer 57

stepwise evolution of antibiotic resistance

Answer 58

**retroviruses often carry oncogenes** - good for virus if the host cell just keeps on making copies ex. **Rous's sarcoma virus** & **cervical cancer caused by HPV virus**

Answer 59

**myeloid white blood cells**: innate immune system, pre-programmed in all individuals to engulf or destroy pathogens - *phagocytes and macrophages* **lymphoid white blood cells**: part of the *adaptive immune system* which learns and adapts to pathogens to reduce change of second infection from the same pathogen - *B cells and T cells*

Answer 60

**B cells**: produce antibody molecules with exquisite specificity and affinity for pathogens **T cells**: can recognize and kill virus infected cells to prevent the spread of infection

Answer 61

consist of 2 **heavy chain** and 2 **light chain** proteins covalently linked by *disulfide bonds* **Fab**: variable region that binds to a specific *antigen* **Fc**: constant region; binds cells and molecules of the immune system

Answer 62

*terms are usually used interchangeably but there are some differences* **phagocytes**: more general term for any cell that can engulf and destroy foreign particles, including pathogens. **macrophages**: specific type of phagocyte that are larger and more long-lived - also more specialized in their function and play a role in both the innate and adaptive immune responses

Answer 63

**agglutination**: antibodies can clump together multiple antigens, making it easier for phagocytes to clear them. **precipitation**: antibodies can bind to soluble antigens and cause them to precipitate out of solution. **complement fixation**: antibodies can activate the complement system, which is a group of proteins that can lyse bacterial cells (basically drill into them and pop them from the inside)

Answer 64

binds to the specific antigen (like lock and key) **determines**: - *specificity*: Fab region determines which specific antigen the antibody will bind to - *affinity*: Fab region also determines how strongly the antibody will bind to the antigen (higher affinity means tighter bond) **CDRs (complementary-determining regions)**: hypervariable loops within the antibody's Fab region that directly contact the antigen - *contribute significantly to the antibody's ability to bind a specific antigen with high affinity*

Answer 65

**VDJ recombination**: mechanism for generating antibody diversity (crucial outcome is formation of B-cell receptors) - antibody genes in the genome are made of multiple V (variable), D (diversity), and j (joining), and constant region exon modules - *VDJ shuffles these regions* - molecules are edited *by recombination* at the *DNA LEVEL* - this process occurs in B cells during their development in the bone marrow - results in unique combination of V, D, and J segments in mature antibody gene, leading to vast array of possible antibody specificities - heavy chain and light chain rearrangements

Answer 66

**allelic exclusion**: mechanism for ensuring that each B cell produces only one type of antibody - each B cell has 2 alleles for each antibody chain (maternal and paternal) just like other genes - however, *only one allele* for each chain undergoes rearrangement - *ensures that each B cell produces only a single type of antibody with a unique specificity*

Answer 67

enzymes that do the genomic editing in VDJ recombination - essential for development of B and T cells also are similar to transposons!! - phylogenetic analysis suggests that our porto-vertebrate ancestor acquired these enzymes through **horizontal gene transfer** (transfer of genes to unrelated organisms)

Answer 68

- originate from **hematopoietic stem cells in the bone marrow** begin as **Pro B cell** → RAG-mediated heavy chain rearrangement → **Pre B cell** → light chain rearrangement → **Immature B-cell** - throughout this process, **VDJ recombination** is taking place → unique blueprint for the antibody the B cell will eventually produce - most importance outcomes: **B cell receptor (BCR)**: this is what determines which cells will be killed using negative selection and which ones will proceed to the **spleen** for further maturation - if they recognize self-antigen → apoptosis *all happening in the bone marrow*

Answer 69

**affinity maturation**: B cells encounter foreign antigens and undergo affinity maturation → process that *enhances binding strength between BCR and antigen* - involves introducing *mutations in the antibody genes* (using AID - cytidine deaminase), particularly in the CDRs, the regions that directly contact the antigen * like fine-tuning the lock to perfectly match the key* ways of affinity maturation: **Somatic Hypermutation**: involves introducing additional mutations in the antibody genes, further increasing the diversity and affinity of antibodies **Class Switching**: Initially, B cells produce IgM antibodies (first line of defense) - However, can switch to producing other antibody classes like IgG (most prevalent in bloodstream) - IgA (mucosal) - IgE (Fc stimulates allergic response) - class switching depends on the type of immune response required.

Answer 70

**somatic hypermutation**: mutations are introduced in the antibody genes (specifically in the VDJ region) - process is triggered by **activation of the B cell receptor (BCR)** **activation-induced cytidine deaminase (AID)**: key enzyme responsible for generating these mutations *steps*: 1. AID binds to RNA poly II (enzyme responsible for transcribing DNA into RNA) 2. as RNA poly II transcribes the antibody gene, AID hitches a ride and introduces mutations in the DNA sequence 3. AID's primary action is **deamination** (removing amino group from a molecule) - AID specifically dominates C to U → mismatch → body tries to fix it but it causes mutations 4. mutations lead to more affinity for antigen in the mutated antibodies

Answer 71

because of antibodies remarkable **specificity and affinity**, they are powerful tools in diagnostics and therapeutics **ELISA (enzyme-linked immunosorbent assay)**: widely used, uses antibodies to detect presence of specific proteins or antigens in a sample - relies on ability of antibodies to bind tightly to their target antigens *their high affinity allows for detection even at low temperatures, enhancing sensitivity of diagnostic tests*

Answer 72

**monoclonal antibodies (mAbs)**: antibodies produced from a single clone of B cells → results in population of antibodies that bind to the same epitope of the same antigen - different from **polyclonal antibodies**: mix of different antibodies that recognize various epitopes on the antigen **importance**: - target a single, well-defined epitope → minimizes cross reactivity w other molecules & potential side effects - therapeutic potential: can *block receptors* (bind to receptors on surface of cell and prevent them from interacting with ligands →stop cell division), can *flag cells for destruction* (bind to target cells and mark them for destruction), can *neutralize pathogens* - any medicine using mab's name ends with mab!!

Answer 73

**hydridoma technology**: traditional method, fuses antibody-producing B cell with immortalized myeloma cells → hybridomas can be grown in culture & produce large quantities of mAbs **phage display**: more recent technology, involves creating libraries of Fab genes displayed on bacteriophages, phages are then screened against target antigen to identify those carrying the desired antibody

Answer 74

**MHCs**: found in all vertebrates **HLA (human leukocyte antigens)**: human version of MHCs (only specific to humans) - term "HLA" was first coined b/c these molecules were first identified on white blood cells (leukocytes) and were recognized for their role in tissue rejection during transplantation

Answer 75

**MHC Class I**: main function is to present endogenous antigens (typically derived from intracellular pathogens like viruses) to **CD8+ killer T cells** → kills infected cell - *expressed on surface of all nucleated cells in the body* **MHC Class II**: main function is to present exogenous antigens (typically derived from extracellular pathogens or foreign substances that have been engulfed by APCs) to **CD4+ helper T-cells** → T cells secretes **cytokines**→ stimulate B cells to produce antibodies and activate other immune cells - *primarily expressed on surface of specialized immune cells called **antigen presenting cells (APCs)** like macrophages, dendritic cells, and B cells*

Answer 76

protein complexes found on surface of T cells that recognize and **bind to specific MHC complexes** - each T cell expresses a unique TCR that can recognize a specific combination of MHC molecule & peptide antigen **have dual specificity**: must recognize both MHC molecule & the peptide antigen being presented - ensures they only respond to infected cells and not to healthy cells displaying self-antigens **structually similar to antibodies** and also generated through VDJ recombination

Answer 77

**polymorphism**: highly polymorphic → many different alleles (variants) within population - high degree of polymorphism ensures that different individuals present wide array of peptides → more ability to respond to diverse pathogens **co-dominance**: both MHC alleles are inherited from each are expressed *equally*→increases diversity even more b/c each individual can express up to 6 MHC I molecules and up to 12 MHC II molecules **role in transplantation**: major targets of immune system during organ transplantation **linkage and haplotypes**: MHC genes are located close to each other on *chromosome 6* → often inhertied together as a unit called **haplotype** → more possiblities of MHC genes

Answer 78

*occurs in the thymus* **negative selection**: T cells that recognize self-antigens are killed **positive selection**: makes sure T cells that can bind to MHC molecules

Answer 79

contagious cancer that affects Tasmanian devils, spread through bites and causes tumors on face and neck - cancer cells evade immune system bc they **express MHC molecules similar to host** → difficult for immune system to recognize them as foreign

Answer 80

protein found on surface of T cells when binds to **PD-L1 ligand** (expressed on tumor cells) → inhibits T-cell's activity to kill the tumor cell → mechanism used by cancer cells to evade immune system *Anti-PD-L1 and anti-PD-1 antibodies are anti-cancer drugs* (they block interaction between the PD-L1 ligand and the PD-1 receptor)

Answer 81

T-cells can kill cancer cells by recognizing antigens presented on MHC I molecules on surface of cancer cells, however they can fail sometimes because of: - **negative selection**: T cells that recognize self-antigens were eliminated during T-cell development & cancer cells often present self-antigens - **low antigen expression**: some cancer cells express tumor antigens at very low levels → difficult for T-cells to detect them - **immune evasion mechanism**: cancer cells can evolve mechanisms to evade the immune system, expressing PD-L1 to inhibit T-cell activation

Answer 82

- engineer T-cells to recognize specific cell types - engineer the **dendritic cells** that activate T-cells

Answer 83

type of immunotherapy that involves engineering T cells to express chimeric antigen receptors (CARs) **CARs**: antibody that binds a cell-surface receptor expressed on tumor cells to a T-cell activating receptor - gene encoding CAR is inserted into T cells harvested from patient and engineered T cells are re-injected back into the patient - these engineered T cells can now recognize tumor cells via the CAR-T receptor and kill them * was first used on Emily Whitehead (12 year old leukemia patient) at age 6 who has been cancer free for 5 years now*

Answer 84

**coronaviruses**: enveloped viruses with crown-like appearances - possess **single stranded RNA genome** (ssRNA) that can be directly translated into proteins - **key structural components**: spike protein, nucleocapsid, membrane, and the envelope *spike protein is crucial for viral entry by binding to the host cell's ACE2 receptor*

Answer 85

using **RT-qPCR**

Answer 86

large protein encoded by the coronavirus genome that is essential in the coronavirus life cycle - poly protein is one single lone polypeptide chain but is **cleaved into 16 smaller proteins** called **non-structural proteins (NSPs)** key NSPs: - **NSP3 and NSP5**: act as proteases, enzymes that break down other proteins - responsible for cleaning the poly protein into individual NSPs - **RNA directed RNA polymerase**: enzyme crucial for replicating virus's RNA genome

Answer 87

protease enzyme that breaks down proteins, for entry, SARS-Cov-2 needs to be **cleaved by this protease** interestingly, **omicron variant bypasses this need** = why it can efficiently infect cells in the upper respiratory tract (making it more widespread but less deadly)

Answer 88

antigens in vaccines are packaged with preservatives, stabilizers, and immune stimulants (adjuvants)

Answer 89

use weekend or dead pathogens to elicit immune response - **major challenge**: need to grow lots of virus and kill it or inactivate it without losing immunogenicity AND without harming people

Answer 90

**protein vaccines**: directly inject recombinant viral proteins to trigger antibody production - *since proteins do not invade cells, may not get a strong T-cell response* **viral vector vaccines**: put SARS-Cov-2 spike protein gene into crippled adenovirus genome - *stimulates both antibody AND strong T-cell responses* **mRNA vaccines**: deliver synthetic mRNA encoding the spike protein, prompting cells to produce the antigen and trigger an immune response - considered safer and faster than traditional approaches.

Answer 91

RNA is fragile AF! **fix by Dr. Katalin Kariko**: to use modified RNA where the U base is modified → RNA translates correctly but is resistant to degradation

Answer 92

researchers discovered that the **spike protein exists in different conformations** (shapes) -stabilizing spike protein in **pre-fusion conformation**, using mutations like **S-2P** → elicit antibodies to closed spike → prevent binding to ACE2 → neutralize virus

Answer 93

pathogen can evade antibodies by mutating the binding site → even **one amino acid change can prevent antibody binding** (b/c antibodies have very high specificity) - *acquire mutations near ACE2 binding site so reduce binding to neutralizing antibody, but maintain binding to ACE2 receptor* - examples are the emergence of variants like Alpha, Gamma, and Omicron

Answer 94

**independent emergence** of similar mutations in different viral lineages, such as the E484K mutation - **N501Y and K417N** bind ACE2 even better than wild-type! highlights the selective pressure exerted by the immune system and the virus's ability to adapt

Answer 95

it possessed numerous mutations in its spike protein, esp in the region that binds to the ACE2 receptor - allowed it to **evade neutralizing antibodies** also had **altered cellular tropism**: infected cells in the upper respiratory tract

Answer 96

neutralizing antibodies primarily block viral entry, but T-cells eliminate infected cells (control spread of virus & prevent severe illness) **omicron retained most of the classic spike protein sequence**: meant that T-cells that had memory before (from vaccination) could still recognize and target Omicron-infected cells

Answer 97

**neutralizing antibodies**: directly block viral entry into cells **non-neutralizing antibodies**: agglutination & precipitation - can bind to multiple virus particles, causing them to **clump together = makes it easier for phagocyte white blood cells** to clear the virus from the body (agglutination) - can also cross-link viral proteins, forming **large insoluble complexes that precipitate out** of solution