biomi 2600 quiz 3

what does somatic hypermutation require?

"activation-induced cytosine deaminase" (AID) and an enzyme that excises DNA containing U residues

IgM can form complexes that have ___ heavy chains

10

IgG has ___ heavy chains

2

if you use PCR and cycle it 20 times, how many copies of the amplified fragment will you have per input molecule?

2^20 (bc 2 strands and amplify 20 times)

IgA can form complexes that have ___ heavy chains

4

commensalism

A relationship between two organisms in which one organism benefits and the other is unaffected

mutualism

A relationship between two species in which both species benefit

In PacBio sequencing, DNA polymerase uses a template DNA strand to synthesize a complementary strand. What is true of each cycle of DNA synthesis? (the video link on the powerpoint slide may be useful)

A. Both the correct (complementary) dNTP analog and the three incorrect analogs can all diffuse into and out of the active site of the DNA polymerase. * B. The correct base forms Watson-Crick base pairs with the template base, while incorrect bases cannot do so. * C. The correct dNTP analog lingers at the active site for several milliseconds before the DNA polymerase makes a covalent bond. * D. When the covalent bond is formed the new base is incorporated, and a molecule containing the fluoresent dye and a pentaphosphate group is released. The molecule containing the dye rapidly diffuses out of the active site and out of the chamber. * E. Fluorescence must be measured in the interval between binding of the dNTP analog and formation of the covalent bond. * H. Because each chamber has only a single DNA molecule, there is no need to maintain synchrony among a population of molecules, so extremely long DNA sequences can be determined. *

interaction between APC and a helper t cell

APC takes up antigen, degrades and displays it complexed the MHC II protein this alerts a t helper cell but only if its TCR can also bind the same antigen

How does immunization work?

Activates the immune system with a vaccine; some are killed vaccines others are live but weakened (attenuated) antigens; they cannot produce disease-are avirulent, when animal is exposed to the antigen, memory cells initiate a rapid response with protection some vaccines are good for life other need to be boostered in all, produces memory cells

IgD

Attached to B cells Activates B cells

when does somatic hypermutation occur?

B cells are activated by helper T cells

the protease papain can cut the heavy chain generating:

Fab and Fc

C1 complex will bind to an IgG antibody at the _____ portion

Fc

the PCR-based detection of person thought to have HIV would NOT require....?

HIV agar media

what are the five classes of antibodies?

IgA, IgD, IgE, IgG, IgM

memory cells ensure a faster response like ___

IgG

an antibody was found to bind to ten antigens at one time.... which antibody was it?

IgM

plasma cells secrete large amount of soluble antibody like ___

IgM

which antibodies can form multimers?

IgM and IgA

when the infection first happens, which antibody type dominates? what happens later?

IgM dominates then IgG which has a better affinitty

during the course of an intestinal infection, the B cells undergo class switching - what kind?

IgM to IgA

if a cell wants to present an antigen to a cytotoxic t cell, which receptor does it use?

MHC I

what is the best way to construct long stretches of DNA sequences from really short ones?

PacBio or Oxford Nanapore sequencing

genes for heavy chain antibody production consist of ___ segments

VDJ

genes for light chain antibody production consist of ___ segments

VJ

What kind of antigen would stimulate naive B-cell proliferation and differention without the help of a T cell

a highly repetitive lipopolysaccharide molecule form Proteus vulgaris

what does the ability of a B cell to switch form synthesizing IgM to IgG require?

a programmed deletion of a portion of the gene that encodes the antibody heavy chain

what is granzyme B

a protease that indirectly unleashes an DNase and other proteases

sebaceous glands in an inactive form can be made active by _____ or a _____

a strong base OR a dedicated bacterial enzyme

pathogenesis

a symbiosis that harms the host

IgE

allergic reactions

what is the segment of antigen that is capable of eliciting an immune response?

antigenic determinant of epitope

how are cells killed by cytotoxic T cells?

antigens from within the infected cell are degraded to peptides which bind to MHC then they are recognized by the t cell receptors of the cytotoxic t cells then cytotoxic t cells release proteins that kill the infected cell (apoptosis)

pentameric IgM is made when

at early stages of an immune response

Subgingival gum disease

bacterial MAMPS are detected by TLRs gum epithelial ells release beta defensins to inhibit colonization gum epithelial cells release the chemokine IL8 which recruits neutrophils to the sites of colonization large numbers of neutrophils migrate to the epithelium and can lead to chronic inflammation porphyromonas gingivalis, a member of the "red complex", is frequently found in patients suffering from gingivitis P gingivitis can inhibit TLR4, so that the epithelium no longer detects lipopolysaccharide Pgingivalis can inhibit IL8, thus decreasing the chemotaxis of neutrophils to the site of inflammation

how do antibodies help phagocytic cells bind and engulf bacteria?

bacterial cells become opsonized and they are bound to various host proteins: antibodies, complement C3b, etc antibodies have a constant region that bind to an Fc receptor not he phagocyte then phagocytosis follows

a diet containing formula and table food was associated w a large increase in _____

bacteriodetes

billions of antibodies exist and they all exist _____ infection

before

if an activated cytotoxic t cell is trying to kill of an influenze infection, what would it do?

bind to infected host cells then release perforin and granzymes

how are B cells activated

capping - does not require T cells or interacting w helper t cells

what does the capping of B-cell receptors on the surface of an antigen-exposed B cell cause?

cell signaling cascade including cell proliferation and differentiation into plasma cells and memory cells

polonies

clusters of PCR products derived from a single molecule of nucleic acid

herd immunity protects against ______ diseases

contagious

what does somatic hypermutation cause?

conversion of C residues to U huge elevation in point mutations in the targeted DNA causes the rapid evolution of B cells whose antibodies have improved affinity for antigen

if a host cell was infected by a virus and then presented fragments of the viral protein on its surface, what would will the host cell? what would not?

cytotoxic t cell would kill (NK would not)

what is the order of steps in a cycle of PCR

denaturation, annealing, extension

what are the five classes of antibodies based on?

differences in CH chain regions

when does the recombination of V,D and j regions occur in B cells?

early development

various sweat glands

eccrine, sebaceous and apocrine

in the Spor, Koren and Key study, the stool contained only ___ at birth and mostly _____ on day 265

firmicutes, bacterioidetes

IgM

first antibody produced in an immune response

in metagenomic analysis, one could use next-generation sequencing to analyze _____ of the microbial community

genomic DNA, mRNA, rRNA and small RNA

apocrine glands

glands that lose small portions of their glandular cell bodies during secretion nutrients for bacteria? develop at puberty

what does terminal deoxynucleotide transferase do?

it synthesizes DNA in a template-independent fashion during somatic recombination of antibody genes

what are the two ways used by natural killer cells to detect virus-infected host cells?

lack oh MHC-I Or antibodies bound to cell surface

how does colonization of teeth by biofilms of bacteria lead to demineralization of enamel and bone?

low oxygen tensions near the tooth surface favor a fermentative metabolism organic acids produced by fermentation are retained within the biofilm and diffuse slowly steptococcus mutants and others, efficiently import dietary sugars such as sucrose

what are the two types of cells that present antigens bound to MHC II?

macrophages and neutrophils

what does the oxford nano pore DNA sequencing the use of?

membrane w very low conductivity a proteinaceous pore that was derived from a pore-forming toxin a DNA helicase protein a long DNA fragment, possibibly containing a hairpin loop at one end a sensitive instrument to detect fluctuations in ion flow through the pore

B cells have ________ antibodies while plasma cells have _____ they start the same but are made different by _____

membrane-associated, secreted slicing

IgA

mucosal immunity

ex: a host cell is infected by a virus that blocks all MHC class I from the cell surface - what kills the cell?

natural killer cells

ex: a host cell is infected by a virus that causes the cell to synthesize a viral protein on the cell surface (also the host has circulating antibodies against the viral protein) what kills the cell?

natural killer cells

how do antibodies protect the host?

neutralization agglutination stimulating phagocytosis

when cysteine are INSIDE of the cell do they form covalent disulfide bonds?

no

is it bad that the recombination of dna to form antibodies is sloppy?

no bc generates a lot of diversity

where does somatic hypermuttaion occur?

only in B cells in the DNA that encodes the variable regions of heavy and light chains

biofilms are aggregates of bacteria that create gradients of

oxygen, nutrients, wastes and antibiotics

humoral immunity

pathogens release "antigens" whichh are recognized by binding to specific host recpetors called antibodies of Igs

how do NK cells kill?

perforins and granzymes to induce apoptosis of virally infected or tumor cells

bacteria fixed in a biofilm and fixed in space and held apart by

polysaccharides, proteins, lipids and extracellular dna (form lysed bacteria)

most skin-colonizing bacteria are gram-______ and _____ resistant

positive, desiccation

classical pathway

requires the binding of an antibody to a pathogen complement activation C3b covalently bound to surface compounds of pathogen recruitment of inflammatory cells/opsonization of pathogens/perforation of pathogen cell membrane death of pathogen

dimeric IgA is

secreted into tears, saliva, GI tract, urinary tract, milk, etc

IgG

the most abundant class of antibodies in serum crosses placenta

how it is possible for a B cell to synthesize a membrane-associated antibody and then differentiate into a plasma cell that secretes virtually the same antibody?

the primary transcript encoding the heavy chain can be spliced in two different ways

anti-HIV antibodies are best at binding to viral proteins when...

the virus is extracellular within the bloodstream

how are NK cells are a part of both innate and acquired immunity?

they have Fc receptors and can kill host cells that have been opsonized by antibodies (acquired) recognize lack of MHC (innate)

what do the dNTPs in PacBio sequencing consist of?

they have fluorescent dyes that do not interfere with polymerization and an Unmodified deoxyribose group

what do the dNTP analogs in illumina sequencing consist of?

they have fluorescent dyes that do not interfere with polymerization but they do have a modified 3' deoxyribose that blocks further polymerization

how do b cells switch the type of antibodies they make?

they use permanent DNA deletions or slicing the mRNA

what do interferons do?

they warn nearby cells of a viral infection, cause nearby cells to produce a double strand RNase, cause nearby cells to temporarily stop protein synthesis, cause nearby infected cells to undergo apoptosis

how are antibodies generated by random joining of DNA segments?

uses variable, diversity and joining regions along w constant regions

are the dyes and modified carbon in the dNTP analogs of illumine sequencing removable?

yes