SCIFOM Exam One- PNWU 2025 - Jacob's Deck

How is infant respiratory distress syndrome treated?

1. Surfactant replacement 2. Oxygen 3. Ventilation 4. Antenatal corticosteroid administration (to the mother)

What factors affect enzyme activity?

1. Temperature 2. pH 3. Substrate Concentration 4. Product Concentration

What are two major roles of Microtubules

1. Transport of intracellular goods 2. movement of cargo during cell division.

What type of bond is involved in sugars vs amino acids?

An O-glycosidic bond in sugars An N-glycosidic bond in AA

What form of DNA is most common?

B-DNA

Which Amino Acid forms disulfide bonds?

Cysteine (Cys)

The Rate of an enzyme reaction is determined by what?

The free energy of activation, not the overall free energy of the reaction

To what does Myosin II bind and in what direction does it move?

The tail of Myosin II can bind to another myosin. Myosin II travels towards the positive pole of actin molecules.

Leach-Nyhan Syndrome

X-linked gene disorder characterized by intellectual disability, signs of cerebral palsy, gouty arthritis, renal calculus and cholelithiasis, and self-injurious behavior Caused by defect in HPRT1 gene for coding hypoxanthine-guanine phosphoribosyltransferase 1, which is involved in recycling purines

What are the biological functions of lipids?

1. storage of energy 2. Cell Structure (membranes) 3. Protection (cushioning) 4. Chemical Regulators (Steroidal hormones) 5. Digestion (Bile acids for fat digestion) 6. Insulation

What is an Enzyme's Velocity if [S] = Km?

1/2 Vmax

Lineweaver-Burk Plot Y intercept is what?

1/Vm

What is the structure of glycerol

3 carbon alcohol with 3 OH groups.

What Temp is ideal for most human enzymes?

37 C

What is the structure of steroids?

4 fused carbon rings labeled A-D. A-C are 6C rings (pyranose) and D is a 5C furanose

Alpha helix has hydrogen bonds between every (Nth) Amino acid

4th

Water accounts for what percent of body weight?

50-75%

Pyranose vs. Furanose

6C ring vs 5C ring

What pH is ideal for most human enzymes?

7.4

What are the six main ways to control Enzyme Activity?

1. Co-Factors 2. Competitive and non-competitive inhibition 3. Allosteric inhibition and activation 4. Phosphorylation 5. Proteolytic cleavage of enzymes 6. Ubiquitination of proteins

What are Allosteric control mechanisms for HMG-CoA reductase (HCR)?

1. High Cholesterol decreases HCR Synthesis 2. High cholesterol increases HCR degradation 3. Low ATP (Glucagon) increases phosphorylation to deactivate HCR synthesis 4. High cholesterol directly feedback inhibits HCR activity. 5. Insulin (in response to high glucose) increases phosphatase to increase cholesterol synthesis. 6. High carbohydrate leads to AcetylCoA production which feeds into cholesterol synthesis.

What is the biological importance of Carbohydrates

1. Immediate energy 2. Stored Energy 3. Structure 4. Cell Signaling.

Name the major subtypes of intermediate filaments

1. Keratin - in epithelial 2. CK19 3. Vimentin - in Fibroblasts 4. Neurofilaments 5. Lamin A and Lamin B - Associated with Nucleus.

Describe Microtubule polymerization

1. Microtubules radiate outwards from the centrosome, polymerization from the gamma-tubulin nucleating sites around the centrosome matrix. 2. The dimers that make up microtubules are composed of an alpha and beta subunit, the alpha-tubular binds to the gamma tubulin initially. 3. Each dimer is bound to either GTP or GDP. When the [GTP] is high, polymerization is favored. When [GTP] = [GDP] tread-milling occurs. (Polymerization at the positive pole and depolymerization at the negative pole)

What are the different types of Lactase Deficiency? What type is most common?

1. Primary lactose malabsorption (most common). 2. Congenital (Rare autosomal recessive disorder 3. Developmental (Lactase activity increases in the fetus, in premature infants (28-32 weeks) they do not have the lactase 4. Secondary Lactose Malabsorption: reduced activity due to damage to the intestinal villi via infection or inflammation

What are some mechanisms of Enzyme regulation?

1. Substrate binding (T vs R conformation 2. Allosteric inhibition and activation. 3. Phosphorylation 4. Protein-Protein interactions (ex: Ca++ / Calmodulin activation of phosphates) 5. Proteolytic Cleavage

how is Km related to affinity?

Km is inversely related to the affinity.

In a Lineweaver Burke Plot Slope is what?

Km/Vmax

At what site does microtubules polymerization start?

Microtubule polymerization starts at the gamma-tubulin nucleating sites which is associated with the centrosome matrix. Alpha-tubulin binds to the Gamma-tubulin, leaving the beta-tubulin to be bound by another alpha-tubulin.

Which major cytoskeletal element has the highest tensile strength

Intermediate Filaments

In what populations is lactose intolerance most and least prevalent?

Most: African blacks at 85-100% and Asians at 90-100% Least: Northern European at 5-15%

What subtype of Myosin is involved in muscle contraction?

Myosin II

What are the three major types of Myosin?

Myosin types I, II, and V.

Which amino acid is associated with turns?

Proline

What regulates PKA?

Protein Kinase A is regulated by cAMP. cAMP can be increased by hormonal stimulation such as epinephrine) cAMP in the cell binds the regulatory subunits of PKA and releases the catalytic subunit —> Intracellular phosphorylation cascade and amplification of the signal.

What amino acids are involved in phosphorylation by Kinases? Why?

Serine, Threonine, and Tyrosine. The Phosphate from ATP is bound to amino acids with an available hydroxyl group ((-OH)

What is Chitin, why is it medically relevant?

Similar to cellulose but the bond is N-acetylglucosamine. Present in insects, arthropods, and fungi. Chitin is digested by chitinases, which is a large group of food allergens.

What are mucopolysaccharides? What anatomical components incorporate mucopolysaccharides?

Slimy long unbranded polysaccharides consisting of repeating disaccharide unit of an amino sugar and a uronic sugar. Synovial fluid, vitreous humor, umbilical cord.

Describe cofactors.

Small organic or inorganic molecules required for enzyme activity.

Motif

Small regions of protein 3D structure shared amount different proteins

To what does Myosin I bind?

The Plasma Membrane

Describe prosthetic groups in the context of enzymes. Provide an example

Tightly bound co-enzymes that do not dissociate. Biotin for carboxylases is an example

What medical condition is Tau Protein associated with?

A mutation in Tau protein is associated with Alzheimer's disease, as Tau is a stabilizing protein. When tau dysfunctions it leads to unstable microtubules and disrupted intracellular trafficking within neurons.

What is the basic structure of the Centrosome?

A pair of centrioles arranged perpendicular to one another. Each centriole is composed of trimers of microtubules. The Centrosome is surrounded by the Centrosome Matrix.

What is plectin and what does it do?

A protein associated with Intermediate Filaments Plectin binds intermediate filaments together and to other cytoskeleton elements. Plectin also binds intermediate filaments to the cell membrane to facilitate "Cell Crawling"

Spectrin

A protein that binds Actin to the cell membrane

What is the Lecithin/Sphingomyelin Ratio and why is it important?

A ratio measured from the amniotic fluid. Signifies risk of Infant Respiratory Distress Syndrome (IRDS) 2.4 or greater, lungs are mature 1.5 or less, patient is at risk for IRDS

Describe what it means for an enzyme to be Taut or Relaxed

A relaxed enzyme is bound by an allosteric activator that increases its affinity. A taut enzyme is bound by an allosteric inhibitor that reduces it's affinity.

What is a teratoma? Why are they unique/interesting?

A tumor that arises from all 3 germinal layers (ectoderm, mesoderm, endoderm). A teratoma arises from pluripotent stem cells (often of the ovaries or testes) and is unique due to its disorganized chaos of cell types

vCreutzfeldt-Jakob disease

A variant fatal form of classic Creutzfeldt-Jakob disease, caused by consumption of contaminated meat products.

What is a zymogen? Name some examples

A zymogen is an inactive pro-enzyme. It is activated by proteolytic cleavage. Examples: Digestive enzymes (Trypsinogen), blood clotting enzymes. Zymogen allow regulation of when and where an enzyme is active.

K63 ubiquitination

Alters signaling pathways, Targets autophagy

HPRT1 gene

Codes for hypoxanthine-guanine phosphoribosyltransferase 1, which is needed for purine salvage pathway. Mutation leads to Lesch-Nyhan Syndrome (LNS).

Irreversible Inhibitor. Provide Example

Covalently binds the enzyme, permanently inactivating. Aspirin permanently disrupts clotting capacity of platelets.

Explain the clinical relevance of CK isozymes.

Creatine Kinase (CK) is a dimer which can come in the form muscle-muscle, muscle-brain, or brain-brain. Cardiac tissue is one of few that contains the MB subtype. During an myocardial infarction the MB will be released into the blood. This can be tested to confirm a MI.

What is the Km?

Michaelis constant; the [S] in mg/L required to produce 50% of the Vmax

Which Coenzymes do not weakly bind?

FAD and Biotin

How many protofilaments are in a microtubule?

Thirteen

In a Lineweaver Burke Plot X intercept is what?

-1/Km

Which nucleotides pair and how many hydrogen bonds each?

A:T (2 bonds) G:C (3 bonds)

Describe the polymerization and depolymerization of Actin.

Actin is a polymer of G-Actin (globular Actin), which polymerizes into F-Actin (Filamentous Actin). 1. G-Actin comes as ATP bound G-Actin and ADP bound G-Actin 2. When [ATP-bound G Actin] is high polymerization is favored, when equal the Actin treadmills. 3. G-Actin is added to the pos. end and is removed from the neg. end

How does Allosteric inhibitors and activators impact the Lineweaver Burke Plot?

Activators decrease Km, increasing affinity Inhibitors increase Km, reducing affinity and shifting the dose response to the right. Most activators and inhibitors change the Km but not the Vmax

Which are the non polar hydrophobic amino acids

Alanine and Valine

What is the structure of Glycogen

Branching polymer of glucose, with repeating alpha 1,4 glycosidic bonds with every 10th glucose branching off with a 1,6 glycosidic bond.

Fibrin and Villin

Binds actin filaments together

Non-Competitive Inhibitor. How is Km and Vmax impacted?

Binds allosteric site, inducing conformational change and inhibiting binding of substrate. Vmax decreases, Km is unchanged.

competitive inhibition. How is Km and Vmax impacted?

Binds at the active site. Vmax is unchanged. Km increases

Uncompetitive Inhibitor. How is Km and Vmax impacted?

Binds the ES complex, preventing disassociation of the ES -> E + P. Both Vmax and Km decrease

How does calmodulin work?

Ca ions bind w/ protein calmodulin which has 4 binding sites once 3 out of 4 of these sites have become bound w/ Ca , calmodulin changes its shape and initiates multiple effects inside the cell, including activation or inhibition of protein's involved in the cell's response to the hormone

Capping Proteins

Capping proteins such as Gelsolin and Tropomodulin stabilize F-Actin

What is cellulose? What enzyme degrades it?

Carbohydrate which is present in plant cell walls. Similar to amylose but it has beta 1-4 glycosidic bonds that cannot be digested by humans. It is digested by Cellulase, which is present in a flagellate Symbiotic organism in the termite gut tract.

What are the four biologically important classes of organic molecules

Carbohydrates, Lipids, Proteins, Nucleic Acids

What are the two main types of Immunohistochemistry?

Direct V. Indirect Direct: a labeled antibody binds the antigen of interest Indirect: A labeled antibody binds a secondary antibody which is bound to the antigen of interest. Indirect is more common as it is cheaper.

What two motor proteins travel along microtubules and in what direction do they each move?

Dynein (- or anterograde movement) Kinesin (+ or retrograde movement)

Profilin

Encourages exchange from ADP to ATP-bound G-Actin, stimulating actin polymerization.

Cofilin

Encourages exchange from ATP to ADP- bound G-Actin, stimulating actin depolymerization.

Which are the negatively charged amino acids?

Glutamic acid and aspartic acid.

Which is the smallest Amino Acid?

Glycine

How do statin Drugs work?

Inhibition of the rate limiting step in cholesterol synthesis. Statins inhibit HMG-CoA reductive, preventing the conversion of HMG-CoA to Cholesterol.

What causes the symptoms in lactose intolerance

Lactose is ingested but cannot be digested due to lack of lactase activity. 2. Bacteria ferment the Lactose generating Lactic Acid and various gases including hydrogen gas. The gas production leads to bloating 3. The Lactic acid induces an osmotic effect wherein water rushes into the intestinal lumen —> Diarrhea. 4. Dissension of the intention leads to increased peristalsis and cramping. Increased peristalsis also leads to malabsorption of fats, proteins, and drugs.

What is the medicinal use of Lactulose? Why does it work?

Lactulose is used as a mild osmotic laxative as it is not hydrolyzed in the intestine, instead it is fermented by intestinal bacteria.

What is the role of liver and muscle glycogen?

Liver glycogen serves as an energy store to maintain blood glucose during fasting whereas muscle glycogen serves as an energy store to maintain moderately high intensity exercise.

Which are the positively charged amino acids?

Lysine and Arginine

Describe Coenzymes

Organic molecules derived from water soluble vitamins (NAD, FAD). Typically weakly binds to enzymes.

What drugs inhibit depolymerization of microtubules?

Paclitaxel and Docetaxel

What enzyme removed phosphate groups from proteins?

Phosphatases

What is the monomer composition of Sucrose, Lactose, and Maltose

Sucrose: Glucose + Fructose (alpha 1,4 linkage) Lactose = Galactose + Glucose (beta 1,4 linkage) Maltose = Glucose + Glucose (alpha 1,4 linkage)

What is Infant Respiratory Distress Syndrome?

Surfactant deficiency disorder in newborns. The Surfactant is important in stabilizing the alveolar cells, when the baby is premature the lungs are not fully developed and the Alveoli can collapse. The main component of the surfactant is dipalmitoylphosphatidylcholine (DPPC) - it reduces surface tension, allows effortless expansion. Without it alveoli collapse.

What are the symptoms, diagnosis, and treatment of Lactose intolerance

Symptoms: Bloating, Cramping, Flatulence, Osmotic Diarrhea Diagnosis: H+ breath test positive, reduced stool pH Treatment: Abstaining from dairy, supplementation with lactase pill.

What drugs inhibit polymerization of microtubules?

Vinblastine and Colchicine

What is End-product Inhibition?

When the final product in a metabolic pathway inhibits an enzyme that acts earlier on in the pathway

What are the axes on a Lineweaver-Burk plot?

X-Axis: 1/[S] Y-Axis: 1/V

What are the two main types of starches? How do they differ?

amylose and amylopectin Amylose: long chain carbohydrate. 100s of glucose polymerized in line by alpha 1-4 glycosidic bonds Amylopectin: Branching molecule linked via alpha 1-4 glycosidic bonds with every 20th branching off with a 1,6 glycosidic bond.

What are the four major tissue types?

epithelial, connective, muscle, nervous

What is the Turnover number?

number of substrate molecules an enzyme converts to a product per second

Which are the Aromatic Amino Acids

phenylalanine, tyrosine, tryptophan

What is the Ubiquitin-Proteasome Pathway?

principal mechanism for protein catabolism in the mammalian cytosol and nucleus. Damaged, misfolded, or extraneous proteins are tagged with ubiquitin, which targets the protein to the proteasome which then digests the protein.

K48 ubiquitination

proteasomal degradation: irreversible, permanent

A dipeptide is formed by what kind of bond?

synthesis and condensation reaction

What is Epidermolysis bullosa simplex (EBS)?

•A genetic disorder caused by mutations in keratin genes (skin blisters develop due to skin cell disruption after minor trauma).