★ microbio ; exam 2 content (bio116)

!! i didnt add the extra extra translation drugs yet !! openstax based but heavily referenced from prof slides + his "deep dive" in-lectures! I include 95% of the content because I leave out some obvious stuff like ligase, primary second immune resp, etc.. happy studying :)

plasmid

extra chromosomal DNA that is small and circular, encoding extra functions in prokaryotes

structure of DNA

double helix with weak hydrogen bonds and a nucleotide: deoxyribose sugar, nitrogenous base, phosphate

deoxyribonucleotide

a structure that builds DNA, containing deoxyribose sugar, a nitrogen base, and phosphate

serratia marcesens

a bacteria that prefers room/human temp but exclusively expresses a red color in a temp cooler than 37

restrictions to DNA processes

DNA is antiparallel + DNA polymerase only adds to a pre-existing 3’ end

DNA polymerase

forms bonds and new chains in DNA replication; only builds on 3’ end ; iii builds frm primer and i replaces rna with dna

primase

builds rna primers for DNA replication

dna replication differences between prokaryotes and eukaryotes

eukaryotes have multiple origins of replication, while prokaryotes have one origin of replication

which direction do the polymerases build from AND read from?

build 5’ → 3’ and read 3’ → 5’

topoisomerase

enzyme in dna replication that is involved in relaxing the supercoiling of DNA

quinolone

a antibiotic that inhibits DNA gyrase (gram neg) and topoisomerase IV (gram pos) causing rapid cell death

quinolone structure

2 ringed structure with r groups

bacteriostatic

describes a drug that stalls growth in bacteria

bactericidal

describes a drug that kills the bacteria; lethal

sigma (σ) factor

transcription factor in transcription that helps the process start, many are σ factor specific

rho (ρ) factor

transcription factor in transcription that dissociates RNA polymerase from binding

rifampicin/rifamycin

binds to the subunit of bacterial rna polymerase, specifically blocking the initiation of transcription

fidaxomicin (lipiarmicin)

inhibits the initiation of bacterial RNA synthesis by binding to RNAP before the open promoter complex (RPo) forms

actinomycin D

intercalates into DNA physically blocking movement of RNA polymerase, although it is not specific to bacteria and also affects eukaryotes

streptolydigin

inhibits RNA chain elongation

myxopyronins

inhibit initiation by targeting the RNAP switch region

bicyclomycin

inhibits the transcription termination factor rho

what type of ribosome(s) do prokaryotes and eukaryotes have?

70s : prokaryote, 80s : eukaryote

tetracyclines

binds to the 30S subunit, preventing tRNA from binding to the ribosomal A site

aminoglycosides

30s ribosomal subunit inhibitor that causes the misreading of mRNA and interferes with the proofreading process, leading to premature termination

macrolides

50S ribosomal subunit inhibitor that blocks the polypeptide exist tunnel, stopping elongation

chloramphenicol

50s subunit inhibitor that inhibits peptidyl transferase, preventing peptide bond formation

tetracycline structure

four six-membered ring

aminoglycosides structure

just. think. SUGARRRRRR

chloramphenicol structure

nut screw and chlorines

why is chloramphenicol treatment temporary?

it can cause anemia

what can bacteria do in transcription and translation that eukaryotes cannot? (why do they grow fast?)

both processes can happen simultaneously, which contributes to fast growth while eukaryotes only have it one at a time

induced mutation

a mutation created in the lab as a result of using chemicals (mutagens) or radiation

transposable elements/transposons

“jumping genes”, genes that can jump around,, when inserted, they can alter the genetic makeup of cells

smooth strain

deadly strain of bacteria that has a capsule (virulence factor), inactive when heat-killed

rough strain

strain of bacteria without a capsule, can be killed by immune system

mixing a heatkilled smooth strain with a rough strain in an animal will result in

killing the animal; rough strain picks up the smooth strain’s dna (transformation)

conjugation

transfer of DNA (plasmid) between bacteria via a sex pilus

high frequency transfer

partial transfer of DNA (plasmid) between bacteria via a sex pilus

transduction

where a bacteriophage transmits its DNA into the bacteria

innate immunity

immediate, nonspecific protection that is active since birth ; all animals

adaptive immunity

slow, targeted, specialized response developed after exposure to agents (microbes, toxins, foreign substances) ; vertebrates only

barrier defenses

a part of innate immunity that involves the skin, mucous membranes of respiratory, urinary, + reproductive tracts

saliva

a barrier defense that contains enzymes and antibodies that work against the bacteria found in our teeth

mucociliary escalator

found in the trachea, contains mucus that catches debris that we breathe in

mucous traps

mucus that allows for microbe removal, such as sending collected debris to be killed in a acidic environment (stomach acid)

phagocytosis

process that brings in large particles or other cells; “cell-eating”

toll-like receptors (TLRs)

receptors in phagocytic cells that detect foreign substances and then initiate immune response

neutrophil

type of phagocytic cell that engulfs and destroys pathogens

macrophages

type of phagocytic cell that engulfs and destroys pathogens, first line of defense that comes after neutrophils

dendritic cells

type of phagocytic cell that stimulates development of adaptive immunity

eosinophils

type of phagocytic cell that discharges destructive enzymes

natural killer cells

cells that circulate through the body and detect abnormal cells, releasing chemicals that lead to cell death ; inhibits the spread of virally infected/cancerous cells

antimicrobial peptides

group of peptides that attack pathogens/impede their reproduction as a part of innate defense

interferon

proteins that interfere with viruses by making the host cell release it to be detected by macrophages

complement system of proteins

~30 proteins that causes the lysis of invading cells and helps trigger inflammation

mast cells

type of connective tissue that releases histamine as a inflammatory response; triggers blood vessels to dilate and become more permeable

cytokine

a signaling molecule that enhances the immune response, released by activated macrophages, neutrophils and helper t cells

how do pathogens avoid destruction?

modify their surface to prevent recognition or look like host cells

antigens

substances that elicit a response from a B or T cells

epitope

the small accessible part of an antigen that binds to an antigen receptor

b cells

a type of lymphocyte with Y-shaped antigen receptors that when activated, releases antibodies / immunoglobulin (lg) as a plasma cell and memory cells

major histocompatibility complex (MHC)

host proteins that display the antigen fragments on the cell surface, esp for infected cells for them to get killed

what is ‘self reactivity’ for lymphocytes

as lymphocytes mature to later b/t cells, anything recognized as ‘self’ is destroyed

helper t cells

a type of t cell that responds to nearly all antigens, triggering both humoral and cell mediated responses (cells are activated)

clonal selection

proliferation of lymphocytes where b/t cells undergoes mulitple cell divisions after activation; produces two types of clones

effector cells

short-lived clone from clonal selection that immediately acts against the antigen

memory cells

long-lived clone from clonal selection that can give rise to effector cells if the same antigen is encountered again

plasma cells

a antibody secreting effector cell from B cells

cytotoxic t cell

effector cells in a cell-mediated response that secretes proteins that disrupt the membranes (punch holes), killing the cell via apoptosis

humoral response

a branch of acquired immunity characterized by secretion of antibodies by b cells; helps neutralize/elimatnate toxins and pathogens in blood and lymph

process of humoral response

class II MHC surfaces on infected cell and then antigen receptor from the helper t cell detects it, activating the helper t cell. it then releases cytokines which activates b cells. b cells proliferate, becoming memory b cells and plasma cells

antibody

form of protein that marks pathogens for destruction

neutralization

process where antibodies bind to viral surface proteins preventing infections of a host cells

opsonization

process where antibodies bind to antigens on bacteria creating a target for macrophages/neutrophils, triggering phagocytosis

antigen-antibody complexes

a complex where antigens and antibodies are bound together, and may bind to a complement protein. triggers a cascade of complement protein activation which forms a pore in the foreign cell membrane, leading to lysis

cell-mediated immune response

a branch of acquired immunity that involves specialized t-cells (killer t cells) that destroy affected host cells

cell-mediated immunity process

class I MHC surfaces on infected cell and then antigen receptor from the cytotoxic/killer t cell detects it, activating the cytotoxic/killer t cell. it then releases molecules and enzymes that create pores in the membrane, killing the infected cell

immune memory

adaptive system keeps a record of past pathogens, allowing for a faster, stronger immune response upon re-exporsure

active immunity

immunity that develops naturally when memory cells form clones in response to infection; can develop after immunization/vaccination

immunization/vaccination

when a nonpathogenic form of a microbe or part of a microbe elicits an immune response to an immunological memory

passive immunity

immunity that provides immediate, short term protection; conferred naturally when IgG crosses the placenta from mother to fetus or when IgA passes from mother to infant in breast milk OR artificially by injection antibodies into a nonimmune person

polyclonal antibodies

lab produced antibodies that are products of many different plasma cell clones from a different epitope

monoclonal antibodies

lab produced antibodies prepared from a single clone of b cells grown in culture

immune rejection

when immune defenses from cells are transferred from one person to another, complicating blood transfusions and transplants

what molecule results in immune rejection in tissue graft and organ transplants (not blood type)

MHC molecules; they are genetically different among nonidentical individuals

allergies

exaggerated (hypersensitive) responses to antigens called allergens

process of localized allergies (hay fever)

allergen attaches to receptors on mast cells in first exposure, leading to the production of IgE antibodies. this results in mast cells releasing histamine. symptoms appear the next time allergens enter

IgD

membrane bound class of immunoglobulin that b cells produce

IgM

first soluble class of immunoglobulin that b cells produce

IgG

second soluble class of immunoglobulin that b cells produce; most abundant

IgA

remaining soluble class of immunoglobulin that b cells produce slongside IgE

IgE

remaining soluble class of immunoglobulin that b cells produce alongside IgA

autoimmune diseases

disease where the immune system loses tolerance for self, turning against certain molecules of the body

inborn immunodeficiency

immunodeficiency disease that results from hereditary/developmental defects that prevent proper functioning of innate, humoral, and/or cell-mediated defenses

acquired immunodeficiency

immunodeficiency disease that develops later in life, resulting from exposure to chemical and biological agents

antigenic variation

mechanism where some pathogens can change epitope expression and prevent recognition; ex is influenza, which requires a new vaccine each year

latency

a mechanism where some viruses remain in a host in an inactive state; ex is herpes simplex viruses, which cna be present w/o causing symptoms

human immunodeficiency virus (HIV)

a virus that infects helper T cells, also eluding the immune system through antigentic variation and the ability to remain latent while integrated in host DNA

acquired immunodeficiency syndrome (AIDS)

a syndrome caused by a virus that makes people highly susceptible to opportunistic infections and cancers