Week Three Objectives Flashcards
How is dietary folate converted to an active cofactor?
Folate comes from diet
Folate has poly-glutamate tail that is digested down to mono-glutamate in gut by Dihydrofolate reductase (DHFR)
Folate is reduced to N5-methyl tetrahydrofolate in intestinal epithelial cells by DHFR
FH4 + formate –> N10 formyl FH4
What is the pathway from THF to methylcobalamin?
THF + formate –> 10-formyl THF
reduced to
5,10 Methenyl THF
reduced to
5,10- Methylene THF
reduced to (irreversible methyl trap)
5-Methyl THF (+ cobalamin) –> methylcobalamin
What amino acids can help produce folate intermediates?
THF + histidine –> 5,10-methenyl THF
THF + serine –> 5,10-methylene THF + glycine
*Serine is the most important contributor to the one carbon pool
*Serine, glycine, choline, histidine, and formate contribute to the one carbon pool
*Thymidine nucleotide, purine bases, methionine, and SAM are PRODUCTS of one carbon donations
Describe the one carbon transfer in thymidine nucleotide synthesis and what might be a good anti-cancer therapy
Thymidylate Synthase(TS) reduces Methylene THF to methy during its transfer to dUMP to make dTMP.
This leaves THF in DHF, which then gets reduced to THF by DHFR which can then accepts another one carbon group from serine (hydroxymethlytransferase) to recycle methylene THF
The cycle continues producing more dTMP
**Can inhibit TS or DHFR to target pathway in anti-cancer therapy**
How is dietary Cobalamin converted into a cofactor?
aka Vitamin B12
Dietary B12 first binds to R-binder proteins secreted in the stomach
As R binders are digested, they bind intrinsic factors
This complex is taken up by intestinal epithelial cells and is tranported in the blood as a complex with transcobalamin II protein
What are the two Cobalamin Reactions?
- Adenosyl cobalamin is a cofactor for the rxn where methylmalonyl CoA mutase convers methylmalonyl CoA (from branched/ odd chain A.A.) to Succinyl Co A in order to enter TCA cycle
- Methionine synthase catalyzes the transfer of methy from methylcobalamin to homocysteine to make methionine.
Methione can vind adesoine nucleoside to become SAM. SAM donates methyl group to numerous substrate including precursors to neurtransmitters
Spinda bifida
Folate deficiency
Neural tube development disorder
Heredity Folate Malabsorption
inherited mutation in the proton coupled folate transporter (PCFT)
which is main transporter for dietary folate
Causes a functional folate deficiency despite adequate dietary folate
Megoloblast anemia
folate deficiency
fewer red blood cells, but are larger than normal
lack of thymidine nucleotides delays DNA synthesis, cell mass grows but genome doesn’t replicate, delay in cell division
Pernicious anemia
(megaloblastic anemia + neuro problems)
B12 deficiency
Auto immune disease attack parietal cells, intrisic factor can’t interact with cobalamin so can’t get uptake
Symptoms: megaloblastic anemia, big beefy tounge, autoimmue gastritis, and NEURO EFFECTS (demylination)
Hyperhomocysteinemia
mutations in methionine synthase
linked to cardiovascular and neurological problems
Why is folate metabolism a treatment for cancer?
Cancer cells divide rapidly and have high requirement for deoxynucleotides
Methotrexate is a folate analog that inhibits DHFR
5-FLuorouracil is a uracil analog that inhibits TS
In addition to cancer cells these drugs also kill other rapidly dividing cells- blod cells, epithelial cells, and hair follicles
What is the methyl trap hypothesis?
The only metabolic fate of 5-methyl THF is to loose its methyl to cobalamin
In dietary or functional deficiency of cobalamin, folate becomes “trapped” as 5-methyl THF thus unable to particpate in other one carbon transfers
*Cobalamin deficiency results in a functional folate deficiency becase all folate gets trapped as 5-methyl THF
What are common properities of infectious disease?
Micro organisms
acute onset
transmission
immune response
Common modes of transmission of infectious diseases?
Person to person: air borne, direct contact, sexual transmission
Zooenotic (vector borne)
Soil Borne
Common Source (contaminated water supple, food borne)
What did the germ theory of disease demonstrate?
demonstrated link between microbs and infectious disease
What are Koch’s Postulates?
- Suspect pathogen must be in ALL disease cases, and absent in healthy animals
- Grow pathogen in pure culture **
- Cells from pure culutre must cause disease in healthy animal**
- Suspected pathogen must be re-isolated and shwon to be the same as orginal pathogen
Obstacles: need animal model, and some stuff dificult to grow in culutre
The gene theory of disease
Microbial infections that lead to disease can be viewed as an arms race for replication that in the purest sense is related to the survival of one set of genetic information at the expense of another
Griffith’s Experiment
Smooth (capsule)/ Rough (no capusle)
Live S cells killed, Dead S cells didn’t
Live R cells didn’t
heat killed S cells + live R cells killed
*virulence factors- any molecule of a microogransim that aids in its ability to establish and maintain pathogenic infection
Common Bacterial morphologies
Coccus
Rod
Spirillum
Spirochete
Budding/ appendage bacteria (stalk/ hypha)
Filamentous bacteria
How do you perform and interpret a Gram Stain?
Prepare smear: spread culutre in thin film over slide, dry
Heat fix and stain with crystail violet (all cells purple)
Add iodine (crystalizes violet into wall)
Decolorize with alcohol (gram+ are purple, gram- are colorless)
Counter stain with safranin (gram+ are purple, gram- are pink)
Differences found in prokaryotic and eukaryotic cell structures
Prokaryotic
Aggregated mass of DNA (nucleoid)
Plasmids
Cell wall/ peptidoglycan
No membrane bound organelles
DNA one chromosome, circular, lack histones
Cell division by fission or budding
Eukaryotic
Membrane-enclosed nucleous
No-plamids
No cell wall
Membrane bound organelles
DNA multiple chromosomes, linear, contain histones
Cell division by mitosis or meiosis
Process of binary fission
cell elongation, septum formation, completion of septum, formation of walls, cell seperation
**Populations grow EXPONENTIALLY**
3 enzymes needed for Peptidoglycan Synthesis
Autolysin
Transglycosylase (to link sugars)
Transpeptidase to like peptides
*Autolysis occurs unless new cell wall precursors are spliced into existing peptidoglycan to prevent a break in peptidoglycan integriaty as splice point
**Penicillin binds and block activity of transpeptidase
Describe Glycogen Structure
Glycogen is a polymer of glucose
Two types of carbon carbon bonds in glycogen
(1: 4) linear chains
(1: 6) make branch points
Glycogen syntase adds UDP-glucose to chain until 11 units long
Branching enzyme cleaves a piece of chain off and attaches it in a 1:6 glycosidic linkage- both braches are further extended
Glycogens function in liver and and other tissues?
Glycogen is used as a glucose storage for most cell types
In heart & Skeletal- intracellular glucose buffer, buffer for glucose 6-phosphate for use within cells (depends on how much getting from blood, and how much cell is doing). When cleaving glycogen its use is for ONLY that cell
Liver- Serves as glucose buffer for BLOOD, regulates whole body glucose homeostasis. Used for hepatocyte but is also excreted in blood
Enzymes in glycogenogenesis
Glycogen Synthase- adds UDP glucose on to glycogen core
4:6 transferase (branching enzymes) cleaves a piece of chain off and attaches it in a 1:6 glycosidic linkages
Both branches extended
Advantages of branching in glycogen?
Increases solubility
Make more active ends so glycogenolysis and glycogenesis can happen rapidly
Enzymes in glycogen degradation
Glycogen phosphorylase- cleaves unites of glucose from glycogen chains and adds inorganic phosphate to make glucose-1-phosphate (but can’t cleave glucose with in four units of branch point)
Debranching enzyme- two activities
(4:4 transferase activity) cleaves a 1:4 bond and transfers 3 glucose units to the end of another chain in 1:4 bond
(alpha-1,6-glucosidase activity) hydrolyzes the remaing glucose’s 1:6 bond to release glucose
Regulation of glycogen metabolism Fed vs Fasted state
In Fed State: both are UNphosphorylated, glycogen phosphorylase is inactive, glycogen synthase is active
In Fasted State: both are PHOSPorylated, glycogen phosphorylase is active, glycogen synthase is inactive
Insulin (hepatocyte and skeletal) how it regulates glycogen metabolism
Insulin activates (phosphorylates) protein phosphatase-1 which dephosphorylates glycogen synthase (activating it)
Inhibits (phosphorylates) glycogen synthase kinase-3 (inactiving it)
Glucagon (hepatocyte only)/ Epinephrine beta regulation in glycogen metabolism
cAMP –> PKA –> phosphorylates glycogen synthase (inactive) and glycgoen phosphorylase kinase (active) –> which then phosphorylates glycogen phosphorylase (acitve) –> glycogenolysis –> GLUCOSE
Glycogen regulation in skeletal muscle (non-hepatocyte)
No glucagon receptor
Nerve impulse–> Ca –> Ca/calmodulin dependent kinase –> phosphorylates glycogen phosphorylase kinase –> phosphorylase glycogen phosphorylase (active)
Work –> AMP –> AMPkinase –> glycogen phosphorylase kinase (active) –> glycgoen phosphorylase (active)
Insulin –> phosphorylates protein phosphatase-1 (active) and glycogen synthase kinase 3 (inactive) –> protein phosphatase then dephosphorylates glycogen synthase (active)
GSD 0
mutation/ deficiency in glycogen synthase
Normal glucose tolerance, variable clinical presentation of exercise intolerance, cardia and muscle hypertrophy
GSD 1
deficiency in glucose 6- phosphatase (can’t make all the way back into glucose to leave cell)
Fast hypoglycemia, lactic acidosis
hepatomegaly due to glycogen accumulation
hyperuricemia and hyperlipidemia
Treatment: avoid fasting by frequent feeding, uncooked cornstarch
GSD III
Deficiency of 1,6-glucosidase activity of debranching enzyme
*can make glycogen when eating too many carns, but can’t break it down all the way in fasting state
GSD IIIa : affects liver and muslce
GSDIIIb: only affect liver
Symptoms: fasting hypoglycemia, ketoacidosis, hyperlipidemia, heptomegaly with high ALT/AST
Treatment: frequent high carb meals
GSD IV
mutation in 4:6 transferase activity of branching enzyme, longer than normal brances, liver failure
FATAL
GSD V
mutations in muscle glycogen phosphorylase
late childhood onset of exercise intolerance, myoglobinuria after exercie
Increased creatine kinase, exaggerated increase of creatine kinase and ammonia after exercise (can’t utilize glycogen, swithcing to AA metabolism)
Avoid exercise
Describe various structures associated with human and bacterial viral pathogens
- Genome- ssRNA, dsRNA, ssDNA, dsDNA
- Capsid- protein coat around genome (capsomere), protects nucleic acids, and is responsible for binding host cells if not enveloped
- Envelope- (some, not all viruses) glycoproteins, function is to bind and mediate entry into host cells. “Naked viruses” have no envelope
- Tegument- space between capsid and envelope, protein dense region that surrounds capsid, holds them together
- Virion- infectious particles produced
Compare the exponential growth of bacterial cells with the one-step growth cycle used during viral replication.
• Latent period- externally doesn’t seem like anything is happening, but really transcription/ translation/replication are occurring
o Good period for attack
- Then get rapidly release of virions in ONE STEP (lots of viruses at ONE time)
- Those virions can go off and affect other cells
Describe the plaque assay procedure – how it’s performed and how it’s useful in the quantification of viral particles
- Plaque Assay- one of the most accurate ways to measure virus infectivity and infectious viral particle numbers
- Procedure
o Mixture containing molten top agar, bacterial cells, and diluted phage suspension
o Pour mixture onto solidified nutrient agar plate
o Let solidify, sandwhich of top again and nutrient agar
o Incubate
o Results are phage plaques on a lawn of host cells
Describe each of the following terms as they relate to human viruses and the cells that they infect: transformation, lysis, persistence, latent, reactivation, cell fusion
- Transformation- virus transforms cell into tumor cell
- Lysis- death of cell and release of virus
- Persistence- Slow release of virus without cell death
- Latent- virus present but not replicating
- Reactivation- may revert to lytic infection?
- Cell fusion- didn’t go over?
Describe each of the following terms as they relate to bacteriophages and the cells that they infect: lysis, lysogeny, virulent, temperate, prophage
- Temperate virus- can go lytic or lysogenic?
- Lysis- viral DNA replicates, coat proteins synthesized, virus particle assembled, host cell is lysed open to expose contents
- Lysogeny- viral DNA is integrated into host DNA, lysogenized cell under goes cell division replicating the prophage (integrated genome)
- Prophages conferring virulence factors
Baltimore classification system
CLASS I
dsDNA (+) genome
classical semiconservative replication
Example: Herpres virsues- uses host DdRp to make mRNA
Baltimore Classification System
CLASS II
ssDNA (+) genome
dsDNA intermediate
classical semiconservative, discard (-) strand for packaging
Baltimore classification system
CLASS III
dsRNA (+) genome
transcription of minus strand to make (+) strand
Baltimore Classification System
CLASS IV
ssRNA (+) genome (can be used directly as mRNA)
makes ssRNA (-) and transcribes this to give ssRNA (+) genome
Example: Polio/ Picornaviruses
*needs RdRp, so must do some translation before genome replication
one long ssRNA strand gets cut after translation into individual proteins
Baltimore Classification System
CLASS V
ssRNA (-) genome
makes ssRNA (+) and transcribes this to give ssRNA (-) genome
Example: Influenze/ orthomyoxyviruses
ssRNA (-) released into cytoplasm, transported to nucleous to steal caps and stuff
brings RdRp with it (attached to each segment of genome)
Baltimore Classification System
CLASS VI
ssRNA (+) genome
transcribes (-) strand of dsDNA to replicate genome
(Reverse transcription)
Example: Retroviruses/ HIV
two copies of ssRNA (+) genome, plus RT and integrase in virion
integrase intergrates dsDNA into host genome
Baltimore CLassification system
CLASS VII
dsDNA genome
transcription followed by reverse transcription
General Viral Replication Cycle
Attachment/adsorption
Penetration/ injection
Synthesis of nucleic acid and protein
Assembly and packagine
Release
Identify properties which limit usefulness of a drug class and drugs within a class (toxicity)
- Selective Toxicity- antibiotics need to injure the invading organism while causing minimal adverse effects to the host
- Toxicity- can be due to
o Extension of mechanism of action
• Trimethoprim can inhibit folate metabolism in humans as well as bacteria resulting in bone-marrow
o Unintended consequences
• Vancomycin can stimulate histamine release (red man syndrome)
o Impaired drug metabolism
• Renal failure or hepatic insufficiency result in direct antibiotic effects or drug interaction
Differentiate between prophylactic, pre-emptive, empiric, suppressive, and definitive therapy
- Prophylactic- treating individuals at a high risk of developing an infection to prevent an infection from developing
- Pre-emptive- lab test indicate organism is present but patient is not symptomatic
- Definitive Therapy- pathogen identified (monotherapy, narrow spectrum)
- Suppressive Therapy- after initial disease is controlled, therapy is continued to prevent recurrence
Categorize drugs as bactericidal and bacteriostatic and explain when you would prefer to use bactericidal drugs
- Bacteriostatic- limits growth and if removed the organism can grow again. Usually successful because allows immune system to catch cup
- Bactericidal- 99.9% reduction in bacterial inoculums with 24 hr period of exposure
- **many bactericidal drugs do not work well if the cells are not actively diving
- ** persons with depressed immune systems would not be good canidates for bacteriostatic drugs
Identify patient factors which affect drug absorption, distribution, metabolism, and excretion
- absorption- movement of drug into vascular system, variability in how well drugs are absorbed from the gut
- Distribution- transfer of drug from vascular system to tissue
- Metabolism- transformation of a compound into metabolites (liver) often inactivates or eliminates the drug BUT prodrugs become active
- Excretion- removal of the drug from the body through urine or feces
Identify mechanism through which drugs develop resistance
- Intrinsic resistance- absence or inaccessibility of the target of the drug action
- Acquired drug resistance- genetic variability exists in the population and resistant forms are able to preferential grow in the presence of the antibiotic
o Variability may result from errors during replication
o Transformation of external DNA
o Bacteriophage can introduce new DNA through transduction
o Conjugation- transfer of R plasmid containing several resistance determinant genes
General potential targets for antibiotics
i. Cell wall synthesis (peptidoglycan)
ii. Nucleic acid synthesis
iii. Cell membrane integrity
iv. Metabolic pathways (folate biosynthesis)
v. Protein Synthesis
Antibiotic Drug Resistance- what causes it? and what are some of the mechanisms?
Acquired Drug Resistance- genetic variability exists in the population and resistant forms are able to preferential grow in the presence of the antibiotic **UNDERSTAND DRUG ITSELF IN NOT CAUSING RESISTANCE**
a. Drug enters cell but efflux pump ejects it
b. Drug-inactivating enzyme- enzyme modifies drug that inactivates it
c. Alteration in target molecule
d. Decreased uptake
Purine Synthesis
phosphoribosyl amidotransferase transfers an amine from glutamine to PRPP
Add glycine to make glycinamide ribosyl 5-phosphate
Carbon, nitrogen are added from THF, CO2, glutamine, and aspartate to form inosine monophosphate (IMP)
To make AMP, asaprtate bonds to IMP –> adenyloscuccinate, then fumarate is cleaved off to make AMP
To make GMP, IMP is oxidized to xanthine monophophate. Amine group is transferred from glutamine.
AMP and GMP are phosphorylated to make adenosine triphosphate and guanosine triphosphate
Describe 3 mechanisms by which bacteria can cause disease
- Toxicity- producing toxins
- Host immune response- repsonse of the host to bacteria
- Colonization/ proliferation
Compare the properities of bacterial endotoxins and extoxins
Exotoxins- not part of the structure, released into enviornment: heat labile, specific mode of action, high toxicity, highly immunogenic
Endotoxins- integeral part of the structure itself, not excreted
(Example- LPS): heat stable, general mode of action, low toxicity, poor immunogen, induces fever
Describe three layers of the immune system.
Physical Barrrier- skin, mucous, epithelial layers, normal flora etc.
Innate Immune System- recognizes forgien particles non specifically, mediated by phagocytosis, recognizes PAMPs, complement, interferons (dendritic cell, marcophage, neutrophil, mast cell)
Adaptive Immune System- inducible, needs to learn how to recognize specific pathogens, has memory, takes time to develop (Antigen, BCR, antibody, TCR)
Cytolytic toxins
Exotoxin, makes holes in membranes surrounding cell. Cause efflux of cytoplasmic components, influx of extracellular components
Hemolysin
Hemolysins- type of cytolytic toxin that affects redn blood cell
EXAMPLE: STREP
- Alpha hemolytic- produces hemolysins that damages but doesn’t destroy red blood cells
EXAMPLE: STAPH
- Beta hemolytic- produces hemolysins completely destroys red blood cells
- Gama hemolytic- does not produces hemolysin
AB toxins
- Exotoxin, proteins excreted with two different modes of action, b = binding, a = activity
1. B domain binds to surface of susceptible cells, stays on outside
2. A domain gets released into cytoplasm and shuts down something inside cell (shut down EF-2, which stops all protein synthesis)
EXAMPLES: E. COLI, Corynebacterium diphtheriae
Enterotoxin
exotoxin, secreted into small intestine, causes diarrhea
Neurotoxin
Exotoxin that can block release of excitation signal, (flaccid paralysis) or binds to inhibitory interneurons preventing release of glycine and relaxation of muscle (Tetanus- rigid paralysis)
Superantigen
Exotoxin, foreign molecule that can exploit interaction between T-cell receptor and MHC class II molecules. Links T-cell and MHC class II receptors NON-SPECIFICALLY activates A LOT of T-cells, causes runaway massive whole body inflammation
EXAMPLE: STAPH
Pathogenicity Island
prophage confers additional virulence genes to bacteria
Proliferation of innate immune system
bone marrow cell
myeloid precursor
monocyte/granulcytes
Dendritic cell, macrophage, neutrophil, mast cells
(these sells have PRRs that recognize PAMPs)
Proliferation of Adaptive Immune System
Bone marrow stem cell
lymphoid precursor
B cell/ T cell
B Cells can divide into plasma cells (produce antibodies) and memory cells
Complement
serum proteins, overall goal is to control inflamation
Microorganism can spontaneously activate complement, results in opsonizaiotn and facilited up take of the coated microogranisms by phagocytes.
Virulence Factors of Salmonella
- Enterotoxin (diarrhea) (type of exotoxin excreted into small intestine)
- Type 1 Fimbriae (enhances edherence)
- Endotoxin in LPS layer (fever)- inherent of gram neg
- Injectosome- ticks phagasome to take it into the cell
- Siderophores- gets excreted into near surface environment and takes up Fe (steals Fe from cells) ramps up ability to utilize more complex metabolic pathways
- Anti-phagocytic proteins induced by oxyR- prevent degredation by phagosomes
- O antigen (inhibits phagocyte killing)
- Cytotoxin (inhibits host cell protein synthesis, calcium efflux, adherence)
- Flagellum (motility)
- H Antigen (adherence, inhibits phagocyte killing)
- Vi capsule antigen- inhibits complement binding
- Describe the key features of the Hepatitis C virus (HCV) lifecycle that lead to both its recognition as a foreign pathogen and its ability to bypass the intracellular innate immune response.
RECOGNITION AS FORGIEN PARTICLE
- During replication Hep C makes a dsRNA intermediate.
- This dsRNA molecule is recognized by TLR3 a Toll-like receptor (PRR)
- The dsRNA binds to TLR3, which activates a signaling cascade,
- Downstream IRF3 is phosphorylated, which forms a dimer and is transported to the nucleus
- IRF3 acts as a transcription factor for IFNB (interferon)?
- IFN-B protein turns on genes that set up an anti-viral state (i.e, shuts down metabolic pathways viruses need to survive, and slows down infection so immune system can catch up.
BACK UP PLAN
- If virus gets past TLR3, dsRNA can bind to RIG-I which binds MAVS, which activates NFkB → IFN-beta
- INTRACELLULAR INNATE IMMUNE RESPONSE
BYPASS
• Viral protein NS3/4A cleaves viral protein, but also destroys signaling pathway proteins so can’t produce interferon → don’t get intracellular innate immune response/ antiviral state
Understand how the production of type I interferons in conducted and how their production leads to the antiviral state inside the host.
- Small protein, important in cell signaling, limit the spread of viral infection by the INNATE system
- Type 1 interferons- are produced by cells that have become infected with a virus
- Typer 2- released by activated T
Know the three types of viral associated pathogenesis.
- Cytopathic effect: viral infection disrupts normal cell physiology
- Host immune response: response of the host to the virus casues illness
- Tumorigenesis: viral infection promotes uncontrolled proliferation of infected cells
Know the two types of fungal associated pathogenesis.
- Overgrowth: spread of fungal infection is significant in the cause of illness
- Host immune response: response of the host to the fungus casues illneess
Know the three types of protozoan associated pathogenesis.
- Displacement: tissure displacement/ obstruction due to the growth of protozoa causes illness
- Cytpoathic effect- intracellular protozoa infection disrupts normal cell physiology
- Host immune response: response of the host to protozoa causes illness
Know the three types of heminth associated pathogenesis.
- Displacemnt- tissue displacement/ obstruction due to the growth of helminth causes illness
- Parasite/ Competition: helminth consumes host nutrition
- Host immune response: response of the host to protozoa csuses illneess
